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Lin FY, Stuckert A, Tat C, White M, Ruggieri L, Zhang H, Mehta B, Lapteva N, Mei Z, Major A, Thakkar S, Shum T, Parikh K, Wu MF, Lindsay HB, Scherer L, Shekar M, Baxter P, Wang T, Grilley B, Moeller K, Hicks J, Roy A, Anastas J, Malbari F, Aldave G, Chintagumpala M, Blaney S, Parsons DW, Brenner MK, Heslop HE, Rooney CM, Omer B. Phase I Trial of GD2.CART Cells Augmented With Constitutive Interleukin-7 Receptor for Treatment of High-Grade Pediatric CNS Tumors. J Clin Oncol 2024; 42:2769-2779. [PMID: 38771986 PMCID: PMC11305939 DOI: 10.1200/jco.23.02019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/26/2023] [Accepted: 02/12/2024] [Indexed: 05/23/2024] Open
Abstract
PURPOSE T cells modified with chimeric antigen receptors (CARTs) have demonstrated efficacy for hematologic malignancies; however, benefit for patients with CNS tumors has been limited. To enhance T cell activity against GD2+ CNS malignancies, we modified GD2-directed CART cells (GD2.CARTs) with a constitutively active interleukin (IL)-7 receptor (C7R-GD2.CARTs). METHODS Patients age 1-21 years with H3K27-altered diffuse midline glioma (DMG) or other recurrent GD2-expressing CNS tumors were eligible for this phase I trial (ClinicalTrials.gov identifier: NCT04099797). All subjects received standard-of-care adjuvant radiation therapy or chemotherapy before study enrollment. The first treatment cohort received GD2.CARTs alone (1 × 107 cells/m2), and subsequent cohorts received C7R-GD2.CARTs at two dose levels (1 × 107 cells/m2; 3 × 107 cells/m2). Standard lymphodepletion with cyclophosphamide and fludarabine was included at all dose levels. RESULTS Eleven patients (age 4-18 years) received therapy without dose-limiting toxicity. The GD2.CART cohort did not experience toxicity, but had disease progression after brief improvement of residual neurologic deficits (≤3 weeks). The C7R-GD2.CART cohort developed grade 1 tumor inflammation-associated neurotoxicity in seven of eight (88%) cases, controllable with anakinra. Cytokine release syndrome was observed in six of eight (75%, grade 1 in all but one patient) and associated with increased circulating IL-6 and IP-10 (P < .05). Patients receiving C7R-GD2.CARTs experienced temporary improvement from baseline neurologic deficits (range, 2 to >12 months), and seven of eight (88%) remained eligible for additional treatment cycles (range 2-4 cycles). Partial responses by iRANO criteria were observed in two of seven (29%) patients with DMG treated by C7R-GD2.CARTs. CONCLUSION Intravenous GD2.CARTs with and without C7R were well tolerated. Patients treated with C7R-GD2.CARTs exhibited transient improvement of neurologic deficits and increased circulating cytokines/chemokines. Treatment with C7R-GD2.CARTs represents a novel approach warranting further investigation for children with these incurable CNS cancers.
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Affiliation(s)
- Frank Y. Lin
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
| | - Austin Stuckert
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Candise Tat
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Mark White
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Lucia Ruggieri
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | - Huimin Zhang
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Birju Mehta
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Natalia Lapteva
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Zhuyong Mei
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Angela Major
- Department of Pathology, Baylor College of Medicine, Houston, TX
| | - Sachin Thakkar
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Thomas Shum
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
- Department of Radiology, Brigham and Women's Hospital, Boston, MA
| | - Kathan Parikh
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Meng-Fen Wu
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Holly B. Lindsay
- Department of Pediatrics Heme-Onc and Bone Marrow Transplantation, Children's Hospital Colorado Center for Cancer and Blood Disorders, University of Colorado Anschutz Medical Campus, Denver, CO
| | - Lauren Scherer
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Meghan Shekar
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Patricia Baxter
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
| | - Tao Wang
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Bambi Grilley
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Karen Moeller
- Department of Radiology, Baylor College of Medicine, Houston, TX
| | - John Hicks
- Department of Pathology, Baylor College of Medicine, Houston, TX
| | - Angshumoy Roy
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
- Department of Pathology, Baylor College of Medicine, Houston, TX
| | - Jamie Anastas
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | - Fatema Malbari
- Department of Neurology, Baylor College of Medicine, Houston, TX
| | - Guillermo Aldave
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | - Murali Chintagumpala
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
| | - Susan Blaney
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
| | - D. Williams Parsons
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
| | - Malcolm K. Brenner
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Helen E. Heslop
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Cliona M. Rooney
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Bilal Omer
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
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Yang J, Feng J, Lv J, Chu X, Wei Y, Zhang Y, Li J, Sun Y, Li G, Jiang T, Huang J, Fan X. PTBP1-mediated repression of neuron-specific CDC42 splicing constitutes a genomic alteration-independent, developmentally conserved vulnerability in IDH-wildtype glioblastoma. Funct Integr Genomics 2024; 24:135. [PMID: 39117866 DOI: 10.1007/s10142-024-01412-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024]
Abstract
Gene co-expression networks may encode hitherto inadequately recognized vulnerabilities for adult gliomas. By identifying evolutionally conserved gene co-expression modules around EGFR (EM) or PDGFRA (PM), we recently proposed an EM/PM classification scheme, which assigns IDH-wildtype glioblastomas (GBM) into the EM subtype committed in neural stem cell compartment, IDH-mutant astrocytomas and oligodendrogliomas into the PM subtype committed in early oligodendrocyte lineage. Here, we report the identification of EM/PM subtype-specific gene co-expression networks and the characterization of hub gene polypyrimidine tract-binding protein 1 (PTBP1) as a genomic alteration-independent vulnerability in IDH-wildtype GBM. Supervised by the EM/PM classification scheme, we applied weighted gene co-expression network analysis to identify subtype-specific global gene co-expression modules. These gene co-expression modules were characterized for their clinical relevance, cellular origin and conserved expression pattern during brain development. Using lentiviral vector-mediated constitutive or inducible knockdown, we characterized the effects of PTBP1 on the survival of IDH-wildtype GBM cells, which was complemented with the analysis of PTBP1-depedent splicing pattern and overexpression of splicing target neuron-specific CDC42 (CDC42-N) isoform. Transcriptomes of adult gliomas can be robustly assigned into 4 large gene co-expression modules that are prognostically relevant and are derived from either malignant cells of the EM/PM subtypes or tumor microenvironment. The EM subtype is associated with a malignant cell-intrinsic gene module involved in pre-mRNA splicing, DNA replication and damage response, and chromosome segregation, and a microenvironment-derived gene module predominantly involved in extracellular matrix organization and infiltrating immune cells. The PM subtype is associated with two malignant cell-intrinsic gene modules predominantly involved in transcriptional regulation and mRNA translation, respectively. Expression levels of these gene modules are independent prognostic factors and malignant cell-intrinsic gene modules are conserved during brain development. Focusing on the EM subtype, we identified PTBP1 as the most significant hub for the malignant cell-intrinsic gene module. PTBP1 is not altered in most glioma genomes. PTBP1 represses the conserved splicing of CDC42-N. PTBP1 knockdown or CDC42-N overexpression disrupts actin cytoskeleton dynamics, causing accumulation of reactive oxygen species and cell apoptosis. PTBP1-mediated repression of CDC42-N splicing represents a potential genomic alteration-independent, developmentally conserved vulnerability in IDH-wildtype GBM.
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Affiliation(s)
- Junjie Yang
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences , Beijing Normal University, Beijing, China
| | - Jing Feng
- Department of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Jing Lv
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences , Beijing Normal University, Beijing, China
| | - Xiaojing Chu
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences , Beijing Normal University, Beijing, China
| | - Yanfei Wei
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences , Beijing Normal University, Beijing, China
| | - Yunqiu Zhang
- Center of Growth Metabolism & Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jiuyi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Yingyu Sun
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences , Beijing Normal University, Beijing, China
| | - Guanzhang Li
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Tao Jiang
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Jinyan Huang
- Biomedical Big Data Center, the First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Xiaolong Fan
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences , Beijing Normal University, Beijing, China.
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53
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Chen F, Zhang Y, Shen L, Creighton CJ. The DNA methylome of pediatric brain tumors appears shaped by structural variation and predicts survival. Nat Commun 2024; 15:6775. [PMID: 39117669 PMCID: PMC11310301 DOI: 10.1038/s41467-024-51276-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024] Open
Abstract
Structural variation heavily influences the molecular landscape of cancer, in part by impacting DNA methylation-mediated transcriptional regulation. Here, using multi-omic datasets involving >2400 pediatric brain and central nervous system tumors of diverse histologies from the Children's Brain Tumor Network, we report hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of somatic structural variant (SV) breakpoints is recurrently associated with altered expression or DNA methylation, respectively, including tumor suppressor genes ATRX and CDKN2A. Altered DNA methylation near enhancers associates with nearby somatic SV breakpoints, including MYC and MYCN. A subset of genes with SV-CGI methylation associations also have expression associations with patient survival, including BCOR, TERT, RCOR2, and PDLIM4. DNA methylation changes in recurrent or progressive tumors compared to the initial tumor within the same patient can predict survival in pediatric and adult cancers. Our comprehensive and pan-histology genomic analyses reveal mechanisms of noncoding alterations impacting cancer genes.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Lanlan Shen
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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54
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LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Allan TJ, Zalusky MPG, Goffena J, Gibson SB, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel MN, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Gupta S, Jones EA, Weisz-Hubshman M, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT, Neale G, Carvill GL, Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, Mefford HC. Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement. Nat Commun 2024; 15:6524. [PMID: 39107278 PMCID: PMC11303402 DOI: 10.1038/s41467-024-50159-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 06/28/2024] [Indexed: 08/09/2024] Open
Abstract
Sequence-based genetic testing identifies causative variants in ~ 50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. We interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 582 individuals with genetically unsolved DEEs. We identify rare differentially methylated regions (DMRs) and explanatory episignatures to uncover causative and candidate genetic etiologies in 12 individuals. Using long-read sequencing, we identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and four copy number variants. We also identify pathogenic variants associated with episignatures. Finally, we refine the CHD2 episignature using an 850 K methylation array and bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate variants as 2% (12/582) for unsolved DEE cases.
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Affiliation(s)
- Christy W LaFlamme
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cassandra Rastin
- Department of Pathology & Laboratory Medicine, Western University, London, ON, N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Soham Sengupta
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Helen E Pennington
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Mathematics & Statistics, Rhodes College, Memphis, TN, 38112, USA
| | - Sophie J Russ-Hall
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Amy L Schneider
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Emily S Bonkowski
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Edith P Almanza Fuerte
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Talia J Allan
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Miranda Perez-Galey Zalusky
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Joy Goffena
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Sophia B Gibson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Denis M Nyaga
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Nico Lieffering
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Malavika Hebbar
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Emily V Walker
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Daniel Darnell
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Scott R Olsen
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mohamed Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Dorit Lev
- Institute of Medical Genetics, Wolfson Medical Center, Holon, 58100, Israel
| | - Tally Lerman-Sagie
- Fetal Neurology Clinic, Pediatric Neurology Unit, Wolfson Medical Center, Holon, 58100, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Kristen L Park
- Departments of Pediatrics and Neurology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Marielle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Gerarda Cappuccio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Nicolas Chatron
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | - Leigh Demain
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - David Genevieve
- Montpellier University, Inserm Unit 1183, Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndrome, Clinical Genetic Department, CHU Montpellier, Montpellier, France
| | - Gaetan Lesca
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, NSW, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Damien Sanlaville
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | | | - Sachin Gupta
- TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Elizabeth A Jones
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Monika Weisz-Hubshman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Genetic Department, Houston, TX, 77030, USA
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, 77030, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC, Australia
- Florey Institute and Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Bekim Sadikovic
- Department of Pathology & Laboratory Medicine, Western University, London, ON, N5A 3K7, Canada.
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada.
| | - Heather C Mefford
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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55
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Fu L, Lao IW, Huang L, Ou L, Yuan L, Li Z, Li S, Hu W, Xi S. Spinal Cord Astroblastoma With EWSR1-BEND2 Fusion in Female Patients: A Report of Four Cases From China and a Comprehensive Literature Review. Am J Surg Pathol 2024:00000478-990000000-00402. [PMID: 39104157 DOI: 10.1097/pas.0000000000002298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Astroblastoma is an extremely rare central nervous system tumor characterized by astroblastic pseudorosettes and vascular hyalinization. Despite these histologic hallmarks, its morphology can vary, occasionally resembling other central nervous system tumors such as ependymoma. A novel tumor entity, astroblastoma, meningioma 1 (MN1)-altered, has been identified, featuring MN1 gene rearrangements typically involving BEN-domain containing 2 (BEND2) as a fusion partner. Most astroblastomas arise in the cerebral hemisphere. Here, we report 4 cases of spinal cord astroblastoma in female patients, all showing Ewing sarcoma RNA-binding protein 1 fusion with BEND2, rather than MN1. These tumors displayed growth patterns akin to traditional intracranial astroblastomas, with three cases demonstrating high-grade histology, including elevated mitotic activity and necrosis. Interestingly, some cases exhibited positive staining for pan-cytokeratin and hormone receptors. DNA methylation profiling clustered three of the four cases with the reference "AB_EWSR," whereas one case exhibited an independent methylation signature near the reference methylation group "AB_EWSR" and "pleomorphic xanthoastrocytoma." Together with the existing literature, we summarized a total of eleven cases, which predominantly affected children and young adults with female predilection. Eight of 10 patients experienced recurrence, underscoring the aggressive nature of this disease. We suggest recognizing a new molecular subgroup of spinal astroblastoma and recommend testing newly diagnosed infratentorial astroblastomas for Ewing sarcoma RNA-binding protein 1-BEND2 fusion.
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Affiliation(s)
- Lingyi Fu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou
| | - I Weng Lao
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University, Shanghai
| | - Liyun Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou
| | - Liqiong Ou
- Department of Pathology, Jiangmen Central Hospital, Jiangmen, China
| | - Lei Yuan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou
| | - Ziteng Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou
| | - Shuo Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou
| | - Wanming Hu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou
| | - Shaoyan Xi
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou
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Pickles JC, Aquilina K, Chalker J, Dahl C, Devadass A, Mankad K, Merve A, Ahmed M, Nicoll JAR, Bloom T, Hilton DA, Sebire NJ, Hargrave D, Jacques TS. Decision making for health-related research outcomes that alter diagnosis: A model from paediatric brain tumours. Neuropathol Appl Neurobiol 2024; 50:e12994. [PMID: 38982613 DOI: 10.1111/nan.12994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 05/20/2024] [Indexed: 07/11/2024]
Abstract
AIMS The question of how to handle clinically actionable outcomes from retrospective research studies is poorly explored. In neuropathology, this problem is exacerbated by ongoing refinement in tumour classification. We sought to establish a disclosure threshold for potential revised diagnoses as determined by the neuro-oncology speciality. METHODS As part of a previous research study, the diagnoses of 73 archival paediatric brain tumour samples were reclassified according to the WHO 2016 guidelines. To determine the disclosure threshold and clinical actionability of pathology-related findings, we conducted a result-evaluation approach within the ethical framework of BRAIN UK using a surrogate clinical multidisciplinary team (MDT) of neuro-oncology specialists. RESULTS The MDT identified key determinants impacting decision-making, including anticipated changes to patient management, time elapsed since initial diagnosis, likelihood of the patient being alive and absence of additional samples since cohort inception. Ultimately, none of our research findings were considered clinically actionable, largely due to the cohort's historic archival and high-risk nature. From this experience, we developed a decision-making framework to determine if research findings indicating a change in diagnosis require reporting to the relevant clinical teams. CONCLUSIONS Ethical issues relating to the use of archival tissue for research and the potential to identify actionable findings must be carefully considered. We have established a structured framework to assess the actionability of research data relating to patient diagnosis. While our specific findings are most applicable to the pathology of poor prognostic brain tumour groups in children, the model can be adapted to a range of disease settings, for example, other diseases where research is dependent on retrospective tissue cohorts, and research findings may have implications for patients and families, such as other tumour types, epilepsy-related pathology, genetic disorders and degenerative diseases.
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Affiliation(s)
- Jessica C Pickles
- Developmental Biology and Cancer & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Histopathology, NIHR Great Ormond Street Hospital Biomedical Research Centre and UCL, London, UK
| | - Kristian Aquilina
- Department of Paediatric Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jane Chalker
- Specialist Integrated Haematology and Malignancy Diagnostic Service-Acquired Genomics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Christine Dahl
- Department of Paediatric Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | | | - Kshitij Mankad
- Department of Paediatric Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ashirwad Merve
- Department of Histopathology, NIHR Great Ormond Street Hospital Biomedical Research Centre and UCL, London, UK
| | - Munaza Ahmed
- North East Thames Regional Clinical Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - James A R Nicoll
- Clinical & Experimental Sciences, University of Southampton, Southampton, UK
- Cellular Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Tabitha Bloom
- Clinical & Experimental Sciences, University of Southampton, Southampton, UK
| | - David A Hilton
- Department of Histopathology, University Hospitals Plymouth, Plymouth, UK
| | - Neil J Sebire
- Developmental Biology and Cancer & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Histopathology, NIHR Great Ormond Street Hospital Biomedical Research Centre and UCL, London, UK
| | - Darren Hargrave
- Developmental Biology and Cancer & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Paediatric Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas S Jacques
- Developmental Biology and Cancer & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Histopathology, NIHR Great Ormond Street Hospital Biomedical Research Centre and UCL, London, UK
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57
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Walker EN, Laws MT, Cozzi F, Quezado M, Brown DA, Burton EC. A case of disseminated spinal astroblastoma harboring a MAMLD1::BEND2 fusion. Neuropathology 2024; 44:278-284. [PMID: 38129983 PMCID: PMC11190029 DOI: 10.1111/neup.12960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Astroblastoma, MN1-altered, is a rare neoplasm of the central nervous system (CNS). This malignancy shares similar histopathological features with other CNS tumors, including ependymomas, making it challenging to diagnose. DNA methylation profiling is a new and robust technique that may be used to overcome this diagnostic hurdle. We report the case of a now 25-year-old female diagnosed with what was initially called an ependymoma located in the cervical spine at the age of 2 years old. After initial resection, the tumor recurred multiple times and within 2 years of diagnosis had disseminated disease throughout the brain and spinal cord. She has now undergone over two decades of treatment, including multiple surgical resections, radiation therapy, and administration of numerous chemotherapeutic agents. In 2021, the patient presented to our institution with lumbosacral radicular symptoms due to enlarging lesions within the lumbosacral spine. Reexamination of formalin-fixed, paraffin-embedded material from the patient's tumor using genomic DNA methylation profiling resulted in a diagnostic change from grade III anaplastic ependymoma to astroblastoma, MN1-altered. This work describes another confirmed case of astroblastoma, MN1-altered, to the growing body of literature.
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Affiliation(s)
- Erin N. Walker
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- University of South Carolina School of Medicine Greenville, Greenville, SC, USA
| | - Maxwell T. Laws
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Cozzi
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Desmond A. Brown
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Eric C. Burton
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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58
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De Wilde J, Van Paemel R, De Koker A, Roelandt S, Van de Velde S, Callewaert N, Van Dorpe J, Creytens D, De Wilde B, De Preter K. A Fast, Affordable, and Minimally Invasive Diagnostic Test for Cancer of Unknown Primary Using DNA Methylation Profiling. J Transl Med 2024; 104:102091. [PMID: 38830578 DOI: 10.1016/j.labinv.2024.102091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 05/16/2024] [Accepted: 05/25/2024] [Indexed: 06/05/2024] Open
Abstract
Currently, we cannot provide a conclusive diagnosis for 3% to 5% of people who are confronted with cancer. These patients have cancer of unknown primary (CUP), ie, a metastasized cancer for which the tissue of origin cannot be determined. Studies have shown that the DNA methylation profile is a unique "fingerprint" that can be used to classify tumors. Here we used cell-free reduced representation bisulfite sequencing (cfRRBS), a technique that allows us to identify the methylation profile starting from minimal amounts of highly fragmented DNA, for CUP diagnosis on formalin-fixed paraffin-embedded (FFPE) tissue and liquid biopsies. We collected 80 primary tumor FFPE samples covering 16 tumor entities together with 15 healthy plasma samples to use as a custom cfRRBS reference data set. Entity-specific methylation regions are defined for each entity to build a classifier based on nonnegative least squares deconvolution. This classification framework was tested on 30 FFPE, 19 plasma, and 40 pleural and peritoneal effusion samples of both known metastatic tumors and clinical CUPs for which pathological investigation finally resulted in a cancer diagnosis. Using this framework, 27 of 30 FFPE (all CUPs) and 16 of 19 plasma samples (10/13 CUPs) obtained an accurate diagnosis, with a minimal DNA input of 400 pg. Diagnosis of the 40 pleural and peritoneal effusion samples is possible in 9 of 27 samples with negative/inconclusive cytology (6/13 CUPs), showing that cell-free DNA (cfDNA) methylation profiling could complement routine cytologic analysis. However, a low "cfDNA - high-molecular weight DNA ratio" has a considerable impact on the prediction accuracy. Moreover, the accuracy improves significantly if the predicted tumor percentage is >7%. This proof-of-concept study shows the feasibility of using DNA methylation profiling on FFPE and liquid biopsy samples such as blood, ascites, and pleural effusions in a fast and affordable way. Our novel RRBS-based technique requires minimal DNA input, can be performed in <1 week, and is highly adaptable to specific diagnostic problems as we only use 5 FFPE references per tumor entity. We believe that cfRRBS methylation profiling could be a valuable addition to the pathologist's toolbox in the diagnosis of CUPs.
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Affiliation(s)
- Jilke De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Ruben Van Paemel
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Andries De Koker
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Sofie Roelandt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Sofie Van de Velde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Nico Callewaert
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Bram De Wilde
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.
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59
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Jugas R, Pokorna P, Adamcova S, Kozelkova K, Knoflickova D, Palova H, Sterba J, Slaby O. Dataset of DNA methylation profiles of 189 pediatric central nervous system, soft tissue, and bone tumors. Data Brief 2024; 55:110590. [PMID: 38974008 PMCID: PMC11226799 DOI: 10.1016/j.dib.2024.110590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/26/2024] [Accepted: 05/30/2024] [Indexed: 07/09/2024] Open
Abstract
Alterations in DNA methylation profiles belong to important mechanisms in cancer development, and their assessment can be utilized for rapid and precise diagnostics. Therefore, establishing datasets of methylation profiles can improve and deepen our understanding of the role of epigenetic changes in cancer development as well as improve our diagnostic capabilities. In this dataset, we generated NGS data for 189 samples of pediatric CNS, soft tissue, and bone tumors. The sequencing libraries were prepared using methyl capture bisulfite sequencing, an effective compromise between whole-genome bisulfite sequencing and array-based methods with a more limited scope of target regions. The larger part of the cohort was processed with the Agilent SureSelectXT Human Methyl-Seq kit (149 samples) and the rest with the Illumina TruSeq Methyl Capture EPIC Library Prep Kit (40 samples). The data presented in this article may help other researchers further elucidate the importance of methylation in diagnosing pediatric CNS tumors, soft tissue, and bone tumors.
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Affiliation(s)
- Robin Jugas
- Department of Biology, Faculty of Medicine and Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czechia
| | - Petra Pokorna
- Department of Biology, Faculty of Medicine and Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czechia
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czechia
| | - Sona Adamcova
- Department of Biology, Faculty of Medicine and Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czechia
| | - Katerina Kozelkova
- Department of Biology, Faculty of Medicine and Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czechia
| | - Dana Knoflickova
- Department of Biology, Faculty of Medicine and Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czechia
- Department of Oncological Pathology, Masaryk Memorial Cancer Institute, Žlutý kopec 543/7, 656 53 Brno, Czechia
| | - Hana Palova
- Department of Biology, Faculty of Medicine and Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czechia
| | - Jaroslav Sterba
- Department of Pediatric Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Jihlavská 20, 625 00 Brno, Czechia
| | - Ondrej Slaby
- Department of Biology, Faculty of Medicine and Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czechia
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60
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Simon M, Kuschel LP, von Hoff K, Yuan D, Hernáiz Driever P, Hain EG, Koch A, Capper D, Schulz M, Thomale UW, Euskirchen P. Rapid DNA methylation-based classification of pediatric brain tumors from ultrasonic aspirate specimens. J Neurooncol 2024; 169:73-83. [PMID: 38769169 PMCID: PMC11269392 DOI: 10.1007/s11060-024-04702-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/30/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND Although cavitating ultrasonic aspirators are commonly used in neurosurgical procedures, the suitability of ultrasonic aspirator-derived tumor material for diagnostic procedures is still controversial. Here, we explore the feasibility of using ultrasonic aspirator-resected tumor tissue to classify otherwise discarded sample material by fast DNA methylation-based analysis using low pass nanopore whole genome sequencing. METHODS Ultrasonic aspirator-derived specimens from pediatric patients undergoing brain tumor resection were subjected to low-pass nanopore whole genome sequencing. DNA methylation-based classification using a neural network classifier and copy number variation analysis were performed. Tumor purity was estimated from copy number profiles. Results were compared to microarray (EPIC)-based routine neuropathological histomorphological and molecular evaluation. RESULTS 19 samples with confirmed neuropathological diagnosis were evaluated. All samples were successfully sequenced and passed quality control for further analysis. DNA and sequencing characteristics from ultrasonic aspirator-derived specimens were comparable to routinely processed tumor tissue. Classification of both methods was concordant regarding methylation class in 17/19 (89%) cases. Application of a platform-specific threshold for nanopore-based classification ensured a specificity of 100%, whereas sensitivity was 79%. Copy number variation profiles were generated for all cases and matched EPIC results in 18/19 (95%) samples, even allowing the identification of diagnostically or therapeutically relevant genomic alterations. CONCLUSION Methylation-based classification of pediatric CNS tumors based on ultrasonic aspirator-reduced and otherwise discarded tissue is feasible using time- and cost-efficient nanopore sequencing.
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Affiliation(s)
- Michèle Simon
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Luis P Kuschel
- Department of Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Katja von Hoff
- Department of Paediatric and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Dongsheng Yuan
- Department of Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Pablo Hernáiz Driever
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Elisabeth G Hain
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Arend Koch
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, a partnership between DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Schulz
- Department of Pediatric Neurosurgery, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Ulrich-Wilhelm Thomale
- Department of Pediatric Neurosurgery, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Philipp Euskirchen
- Department of Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany.
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany.
- German Cancer Consortium (DKTK), partner site Berlin, a partnership between DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany.
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61
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Wagstyl K, Kobow K, Casillas-Espinosa PM, Cole AJ, Jiménez-Jiménez D, Nariai H, Baulac S, O'Brien T, Henshall DC, Akman O, Sankar R, Galanopoulou AS, Auvin S. WONOEP 2022: Neurotechnology for the diagnosis of epilepsy. Epilepsia 2024; 65:2238-2247. [PMID: 38829313 DOI: 10.1111/epi.18028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/05/2024]
Abstract
Epilepsy's myriad causes and clinical presentations ensure that accurate diagnoses and targeted treatments remain a challenge. Advanced neurotechnologies are needed to better characterize individual patients across multiple modalities and analytical techniques. At the XVIth Workshop on Neurobiology of Epilepsy: Early Onset Epilepsies: Neurobiology and Novel Therapeutic Strategies (WONOEP 2022), the session on "advanced tools" highlighted a range of approaches, from molecular phenotyping of genetic epilepsy models and resected tissue samples to imaging-guided localization of epileptogenic tissue for surgical resection of focal malformations. These tools integrate cutting edge research, clinical data acquisition, and advanced computational methods to leverage the rich information contained within increasingly large datasets. A number of common challenges and opportunities emerged, including the need for multidisciplinary collaboration, multimodal integration, potential ethical challenges, and the multistage path to clinical translation. Despite these challenges, advanced epilepsy neurotechnologies offer the potential to improve our understanding of the underlying causes of epilepsy and our capacity to provide patient-specific treatment.
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Affiliation(s)
- Konrad Wagstyl
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
- Developmental Neurosciences, UCL Great Ormond Street for Child Health, UCL, London, UK
| | - Katja Kobow
- Institute of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Pablo M Casillas-Espinosa
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Hospital, Melbourne, Victoria, Australia
| | - Andrew J Cole
- MGH Epilepsy Service, Division of Clinical Neurophysiology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Diego Jiménez-Jiménez
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
| | - Hiroki Nariai
- Division of Pediatric Neurology, Department of Pediatrics, UCLA Medical Center, Los Angeles, California, USA
| | - Stéphanie Baulac
- Institut du Cerveau-Paris Brain Institute-ICM, INSERM, CNRS, Sorbonne Université, Paris, France
| | - Terence O'Brien
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Hospital, Melbourne, Victoria, Australia
| | - David C Henshall
- FutureNeuro SFI Research Centre, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Ozlem Akman
- Department of Physiology, Faculty of Medicine, Demiroglu Bilim University, Istanbul, Turkey
| | - Raman Sankar
- Division of Pediatric Neurology, Department of Pediatrics, UCLA Mattel Children's Hospital, David Geffen School of Medicine, Los Angeles, California, USA
- UCLA Children's Discovery and Innovation Institute, California, Los Angeles, USA
| | - Aristea S Galanopoulou
- Saul R. Korey Department of Neurology, Isabelle Rapin Division of Child Neurology, Laboratory of Developmental Epilepsy, Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Stéphane Auvin
- Université Paris-Cité, INSERM NeuroDiderot, Paris, France
- Pediatric Neurology Department, APHP, Robert Debré University Hospital, CRMR Epilepsies Rares, EpiCARE member, Paris, France
- Institut Universitaire de France, Paris, France
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62
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Kervarrec T, Cheok Lei K, Sohier P, Macagno N, Jullie ML, Frouin E, Goto K, Taniguchi K, Hamard A, Taillandier A, Tallet A, Bonenfant C, Sahin Y, Barry F, Taibjee S, Cokelaere K, Houben R, Schrama D, Nardin C, Aubin F, Doucet L, Pissaloux D, Tirode F, Fouchardière ADL, Balme B, Laurent-Roussel S, Becker JC, von Deimling A, Samimi M, Cribier B, Battistella M, Calonje E, Guyétan S. Wnt/β-Catenin-Activated Nonpilomatrical Carcinoma of the Skin: A Case Series. Mod Pathol 2024; 37:100586. [PMID: 39094735 DOI: 10.1016/j.modpat.2024.100586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 07/08/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
Among skin epithelial tumors, recurrent mutations in the APC/CTNNB1 genes resulting in activation of the Wnt/β-catenin pathway have been reported predominantly in neoplasms with matrical differentiation. In the present study, we describe the morphologic, immunohistochemical, and genetic features of 16 primary cutaneous carcinomas harboring mutations activating the Wnt/β-catenin pathway without evidence of matrical differentiation, as well as 4 combined tumors in which a similar Wnt/β-catenin-activated carcinoma component was associated with Merkel cell carcinoma (MCC) or pilomatrical carcinoma. Among the pure tumor cases, 6 of 16 patients were women with a median age of 80 years (range, 58-98 years). Tumors were located on the head and neck (n = 7, 44%), upper limb (n = 4, 25%), trunk (n = 3, 18%), and leg (n = 2, 13%). Metastatic spread was observed in 4 cases resulting in death from disease in 1 patient. Microscopically, all cases were poorly differentiated neoplasms infiltrating the dermis and/or subcutaneous tissue. In 13 cases, solid "squamoid" areas were associated with a basophilic component characterized by rosette/pseudoglandular formation resulting in a biphasic appearance. Three specimens consisted only of poorly differentiated carcinoma lacking rosette formation. Immunohistochemical studies showed frequent expression of EMA (100%), BerEP4 (100%), cytokeratin 7 (94%), chromogranin A (44%), synaptophysin (82%), and cytokeratin 20 (69%). Complete loss of Rb expression was observed in all but 1 case. Nuclear β-catenin and CDX2 expressions were detected in all cases. Recurrent pathogenic somatic mutations were observed in APC (60%), CTNNB1 (40%), and RB1 (n = 47%). Global methylation analysis confirmed that cases with rosette formation constituted a homogeneous tumor group distinct from established skin tumor entities (pilomatrical carcinoma, MCC, and squamous cell carcinoma), although the 3 other cases lacking such morphologic features did not. In addition, we identified 4 combined neoplasms in which there was a component showing a similar poorly differentiated rosette-forming carcinoma demonstrating Rb loss and β-catenin activation associated with either MCC (n = 3) or pilomatrical carcinoma (n = 1). In conclusion, we describe a distinctive neoplasm, for which we propose the term "Wnt/β-catenin-activated rosette-forming carcinoma," morphologically characterized by the association of rosette formation, squamous and/or neuroendocrine differentiation, diffuse CDX2 expression, Rb loss, and mutations in CTNNB1/APC genes.
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Affiliation(s)
- Thibault Kervarrec
- Department of Pathology, Université de Tours, Centre Hospitalier Universitaire de Tours, Tours, France; "Biologie des infections à polyomavirus" Team, UMR INRA ISP 1282, Université de Tours, Tours, France; CARADERM Network.
| | - Kuan Cheok Lei
- Translational Skin Cancer Research, Department of Dermatology and German Cancer Consortium (DKTK), Partner Site Essen, University Medicine Essen, Essen, Germany, and Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Pierre Sohier
- CARADERM Network; Faculté de Médecine, Université Paris Cité, Paris, France; Department of Pathology, Hôpital Cochin, AP-HP, Centre-Université Paris Cité, Paris, France
| | - Nicolas Macagno
- CARADERM Network; Department of Pathology, Timone University Hospital, Marseille, France
| | - Marie-Laure Jullie
- CARADERM Network; Department of Pathology, Hopital Haut-Leveque, CHU de Bordeaux, Pessac, France
| | - Eric Frouin
- CARADERM Network; Department of Pathology, University Hospital of Poitiers, Poitiers, France; Department of Pathology, University Hospital of Nimes, Nimes, France
| | - Keisuke Goto
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Disease Center Komagome Hospital, Tokyo, Japan; Department of Diagnostic Pathology, Shizuoka Cancer Center Hospital, Nagaizumi, Japan; Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka, Japan; Department of Dermatology, Hyogo Cancer Center, Akashi, Japan
| | - Kohei Taniguchi
- Department of Pathology, Hiroshima City Hiroshima Citizens Hospital, Hiroshima, Japan
| | - Aymeric Hamard
- Department of Pathology, Université de Tours, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Antoine Taillandier
- Department of Pathology, Université de Tours, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Anne Tallet
- Platform of Somatic Tumor Molecular Genetics, Université de Tours, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Christine Bonenfant
- Platform of Somatic Tumor Molecular Genetics, Université de Tours, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Yusuf Sahin
- Department of Pathology, University Hospital of Poitiers, Poitiers, France
| | - Fatoumata Barry
- Department of Pathology, University Hospital of Poitiers, Poitiers, France
| | - Saleem Taibjee
- Poundbury Cancer Institute, Dorchester, Dorset, United Kingdom
| | | | - Roland Houben
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | - David Schrama
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | - Charline Nardin
- Dermatology Department, INSERM 1098, Université de Franche Comté, CHU Besançon, Besançon, France
| | - Francois Aubin
- Dermatology Department, INSERM 1098, Université de Franche Comté, CHU Besançon, Besançon, France
| | - Laurent Doucet
- Department of Pathology, Université de Brest, Centre Hospitalier Universitaire de Brest, Brest, France
| | - Daniel Pissaloux
- Department of Biopathology, Center Léon Bérard, Lyon, France; University of Lyon, Universite Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France
| | - Franck Tirode
- Department of Biopathology, Center Léon Bérard, Lyon, France; University of Lyon, Universite Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France
| | - Arnaud de la Fouchardière
- Department of Biopathology, Center Léon Bérard, Lyon, France; University of Lyon, Universite Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France
| | - Brigitte Balme
- Dermatology Unit, Hospices Civils de Lyon, University Hospital Lyon Sud, Pierre Benite, France
| | | | - Jürgen C Becker
- Translational Skin Cancer Research, Department of Dermatology and German Cancer Consortium (DKTK), Partner Site Essen, University Medicine Essen, Essen, Germany, and Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany; Department of Dermatology, University Clinic Essen, Essen, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Mahtab Samimi
- "Biologie des infections à polyomavirus" Team, UMR INRA ISP 1282, Université de Tours, Tours, France; Department of Dermatology, Université de Tours, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Bernard Cribier
- CARADERM Network; Dermatology Clinic, Hôpitaux Universitaires & Université de Strasbourg, Hôpital Civil, Strasbourg, France
| | - Maxime Battistella
- CARADERM Network; Department of Pathology, APHP Hôpital Saint Louis, Université Paris 7, Paris, France
| | - Eduardo Calonje
- Department of Dermatopathology, St John's Institute of Dermatology, St Thomas' Hospital, London, United Kingdom
| | - Serge Guyétan
- Department of Pathology, Université de Tours, Centre Hospitalier Universitaire de Tours, Tours, France; "Biologie des infections à polyomavirus" Team, UMR INRA ISP 1282, Université de Tours, Tours, France
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63
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Li M, Xu J, Peng C, Wang Z. Deep learning-assisted flavonoid-based fluorescent sensor array for the nondestructive detection of meat freshness. Food Chem 2024; 447:138931. [PMID: 38484548 DOI: 10.1016/j.foodchem.2024.138931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 04/10/2024]
Abstract
Gas sensors containing indicators have been widely used in meat freshness testing. However, concerns about the toxicity of indicators have prevented their commercialization. Here, we prepared three fluorescent sensors by complexing each flavonoid (fisetin, puerarin, daidzein) with a flexible film, forming a fluorescent sensor array. The fluorescent sensor array was used as a freshness indication label for packaged meat. Then, the images of the indication labels on the packaged meat under different freshness levels were collected by smartphones. A deep convolutional neural network (DCNN) model was built using the collected indicator label images and freshness labels as the dataset. Finally, the model was used to detect the freshness of meat samples, and the overall accuracy of the prediction model was as high as 97.1%. Unlike the TVB-N measurement, this method provides a nondestructive, real-time measurement of meat freshness.
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Affiliation(s)
- Min Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Jianguo Xu
- Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, PR China
| | - Chifang Peng
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Life Science and Health Engineering, Jiangnan University, Wuxi 214122, PR China; International Joint Laboratory On Food Safety, Jiangnan University, Wuxi 214122, PR China.
| | - Zhouping Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Life Science and Health Engineering, Jiangnan University, Wuxi 214122, PR China; International Joint Laboratory On Food Safety, Jiangnan University, Wuxi 214122, PR China
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64
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Lau HY, Huang M, Chang KTE, Kuick CH, Takano A. Metastatic Leiomyoma With Malignant Transformation Harboring RAB2A-PLAG1 Fusion-A Case Report and Review With Molecular Analysis. Int J Gynecol Pathol 2024:00004347-990000000-00188. [PMID: 39230504 DOI: 10.1097/pgp.0000000000001058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Metastasizing leiomyoma is a rare condition characterized by the development of benign-appearing smooth muscle neoplasms at extrauterine sites in patients with a history of uterine leiomyoma. These lesions occur most commonly in the lung, with the abdominopelvic and mediastinal lymph nodes being other reported sites. Malignant transformation of metastasizing leiomyoma is extremely rare, with only a few cases described in the literature. We describe a case of metastasizing leiomyoma with malignant transformation in a middle-aged Asian lady, who developed pulmonary metastatic foci 12 years after surgical excision of the original uterine leiomyomata. Molecular analysis showed a common RAB2A-PLAG1 fusion gene and identical single nucleotide variants in both tumor foci, with significantly more pronounced segmental chromosomal copy number variations in one focus showing high-grade features. A comprehensive review of the literature lends support to the hypothesis that the original leiomyomata and the metastatic foci are clonally related, with high-grade features being associated with more complex genomic signatures.
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Affiliation(s)
- Hiu Yeung Lau
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore
- Pathology Academic Clinical Program, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Mingjie Huang
- Department of Cardiothoracic Surgery, National Heart Centre Singapore, Singapore
| | - Kenneth Tou En Chang
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore
- Pathology Academic Clinical Program, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Chik Hong Kuick
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore
- Pathology Academic Clinical Program, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Angela Takano
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
- Pathology Academic Clinical Program, SingHealth Duke-NUS Academic Medical Centre, Singapore
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65
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Priesterbach-Ackley LP, Cordier F, de Witt Hamer P, Snijders TJ, Robe PA, Küsters B, de Leng WWJ, den Dunnen WFA, Brandsma D, Jansen C, Wesseling P, Muhlebner A. Diffuse, IDH-wildtype gliomas in adults with minimal histological change and isolated TERT promoter mutation: not simply CNS WHO grade 4. Acta Neuropathol 2024; 148:12. [PMID: 39073427 PMCID: PMC11286727 DOI: 10.1007/s00401-024-02773-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/19/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024]
Affiliation(s)
- L P Priesterbach-Ackley
- Department of Pathology, University Medical Center Utrecht, Internal Mail No. H04.312, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - F Cordier
- Department of Pathology, University Medical Center Utrecht, Internal Mail No. H04.312, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - P de Witt Hamer
- Department of Neurosurgery, Amsterdam University Medical Centers/VUmc and Brain Tumor Center, Amsterdam, The Netherlands
| | - T J Snijders
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, Utrecht, The Netherlands
| | - P A Robe
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, Utrecht, The Netherlands
| | - B Küsters
- Department of Pathology, Radboudumc, Nijmegen, The Netherlands
| | - W W J de Leng
- Department of Pathology, University Medical Center Utrecht, Internal Mail No. H04.312, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - W F A den Dunnen
- Department of Pathology, University Medical Center Groningen, Groningen, The Netherlands
| | - D Brandsma
- Department of Neuro-Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - C Jansen
- Laboratory for Pathology Eastern Netherlands, LABPON, Hengelo, The Netherlands
| | - P Wesseling
- Department of Pathology, Amsterdam University Medical Centers/VUmc and Brain Tumor Center Amsterdam, and Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - A Muhlebner
- Department of Pathology, University Medical Center Utrecht, Internal Mail No. H04.312, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands.
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66
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Alturkustani M, Walker AD, Castañeda EA, Cotter JA. Utility of OLIG2 immunostaining in pediatric brain tumors with embryonal morphology. J Neuropathol Exp Neurol 2024:nlae082. [PMID: 39067019 DOI: 10.1093/jnen/nlae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024] Open
Abstract
This study evaluates the diagnostic utility of OLIG2 immunohistochemistry for distinguishing between pediatric high-grade gliomas (pHGG) and embryonal tumors (ETs) of the CNS. Utilizing a retrospective pediatric cohort (1990-2021) of 56 CNS tumors, classified initially as primitive neuroectodermal tumors or CNS ET, we reclassified the cases based on WHO CNS5 criteria after comprehensive review and additional molecular testing that included next-generation sequencing and DNA methylation profiling. Our results indicate that OLIG2 immunopositivity was negative or minimal in a significant subset of pHGG cases (6 out of 11). At the same time, it showed diffuse expression in all cases of CNS neuroblastomas with FOXR2 activation (5/5), demonstrating its limited specificity in differentiating between pHGG and ET. Variable OLIG2 expression in other ETs, ATRT, and ETMR suggests the broader diagnostic implications of the marker. Furthermore, incidental findings of OLIG2 positivity in cases traditionally expected to be negative, such as medulloblastoma and ependymoma, introduce an additional layer of complexity. Together, these findings highlight the challenges of relying solely on OLIG2 immunostaining for accurate tumor classification in pediatric CNS neoplasms and underscore the importance of an integrated diagnostic approach.
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Affiliation(s)
- Murad Alturkustani
- Department of Pathology, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
- Department of Pathology, University of Western Ontario, London, ON, Canada
| | - Adam D Walker
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Everardo A Castañeda
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Jennifer A Cotter
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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67
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Lalonde E, Li D, Ewens K, Shields CL, Ganguly A. Genome-Wide Methylation Patterns in Primary Uveal Melanoma: Development of MethylSig-UM, an Epigenomic Prognostic Signature to Improve Patient Stratification. Cancers (Basel) 2024; 16:2650. [PMID: 39123378 PMCID: PMC11312132 DOI: 10.3390/cancers16152650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Despite studies highlighting the prognostic utility of DNA methylation in primary uveal melanoma (pUM), it has not been translated into a clinically useful tool. We sought to define a methylation signature to identify newly diagnosed individuals at high risk for developing metastasis. Methylation profiling was performed on 41 patients with pUM with stage T2-T4 and at least three years of follow-up using the Illumina Infinium HumanMethylation450K BeadChip (N = 24) and the EPIC BeadChip (N = 17). Findings were validated in the TCGA cohort with known metastatic outcome (N = 69). Differentially methylated probes were identified in patients who developed metastasis. Unsupervised consensus clustering revealed three epigenomic subtypes associated with metastasis. To identify a prognostic signature, recursive feature elimination and random forest models were utilized within repeated cross-validation iterations. The 250 most commonly selected probes comprised the final signature, named MethylSig-UM. MethylSig-UM could distinguish individuals with pUM at diagnosis who develop future metastasis with an area under the curve of ~81% in the independent validation cohort, and remained significant in Cox proportional hazard models when combined with clinical features and established genomic biomarkers. Altered expression of immune-modulating genes were detected in MethylSig-UM positive tumors, providing clues for pUM resistance to immunotherapy. The MethylSig-UM model is available to enable additional validation in larger cohort sizes including T1 tumors.
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Affiliation(s)
- Emilie Lalonde
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Schulich School Medicine & Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Dong Li
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathryn Ewens
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carol L. Shields
- Oncology Services, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Arupa Ganguly
- Department of Pathology and Laboratory Medicine, Schulich School Medicine & Dentistry, Western University, London, ON N6A 5C1, Canada
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Godbole S, Voß H, Gocke A, Schlumbohm S, Schumann Y, Peng B, Mynarek M, Rutkowski S, Dottermusch M, Dorostkar MM, Korshunov A, Mair T, Pfister SM, Kwiatkowski M, Hotze M, Neumann P, Hartmann C, Weis J, Liesche-Starnecker F, Guan Y, Moritz M, Siebels B, Struve N, Schlüter H, Schüller U, Krisp C, Neumann JE. Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level. Nat Commun 2024; 15:6237. [PMID: 39043693 PMCID: PMC11266559 DOI: 10.1038/s41467-024-50554-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/11/2024] [Indexed: 07/25/2024] Open
Abstract
Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically heterogenous. The application of omics technologies-mainly studying nucleic acids-has significantly improved MB classification and stratification, but treatment options are still unsatisfactory. The proteome and their N-glycans hold the potential to discover clinically relevant phenotypes and targetable pathways. We compile a harmonized proteome dataset of 167 MBs and integrate findings with DNA methylome, transcriptome and N-glycome data. We show six proteome MB subtypes, that can be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pG3myc), and synapses/immunological processes (pSHHs, pG3 and pG4). Multiomic analysis reveals different conservation levels of proteome features across MB subtypes at the DNA methylome level. Aggressive pGroup3myc MBs and favorable pWNT MBs are most similar in cluster hierarchies concerning overall proteome patterns but show different protein abundances of the vincristine resistance-associated multiprotein complex TriC/CCT and of N-glycan turnover-associated factors. The N-glycome reflects proteome subtypes and complex-bisecting N-glycans characterize pGroup3myc tumors. Our results shed light on targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures.
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Affiliation(s)
- Shweta Godbole
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Antonia Gocke
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon Schlumbohm
- Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
| | - Yannis Schumann
- Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
| | - Bojia Peng
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Mynarek
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Dottermusch
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mario M Dorostkar
- Center for Neuropathology, Ludwig-Maximilians-University, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Andrey Korshunov
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Mair
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Madlen Hotze
- Institute of Biochemistry, University of Innsbruck, Innsbruck, Austria
| | - Philipp Neumann
- Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Hannover Medical School (MHH), Hannover, Germany
| | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | | | - Yudong Guan
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manuela Moritz
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bente Siebels
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nina Struve
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Radiotherapy & Radiation Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Christoph Krisp
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia E Neumann
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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69
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Dyshlovoy SA, Paigin S, Afflerbach AK, Lobermeyer A, Werner S, Schüller U, Bokemeyer C, Schuh AH, Bergmann L, von Amsberg G, Joosse SA. Applications of Nanopore sequencing in precision cancer medicine. Int J Cancer 2024. [PMID: 39031959 DOI: 10.1002/ijc.35100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/25/2024] [Accepted: 06/25/2024] [Indexed: 07/22/2024]
Abstract
Oxford Nanopore Technologies sequencing, also referred to as Nanopore sequencing, stands at the forefront of a revolution in clinical genetics, offering the potential for rapid, long read, and real-time DNA and RNA sequencing. This technology is currently making sequencing more accessible and affordable. In this comprehensive review, we explore its potential regarding precision cancer diagnostics and treatment. We encompass a critical analysis of clinical cases where Nanopore sequencing was successfully applied to identify point mutations, splice variants, gene fusions, epigenetic modifications, non-coding RNAs, and other pivotal biomarkers that defined subsequent treatment strategies. Additionally, we address the challenges of clinical applications of Nanopore sequencing and discuss the current efforts to overcome them.
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Affiliation(s)
- Sergey A Dyshlovoy
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Oxford, UK
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefanie Paigin
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Ann-Kristin Afflerbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annabelle Lobermeyer
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Werner
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute for Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Paediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carsten Bokemeyer
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna H Schuh
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Oxford, UK
| | - Lina Bergmann
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gunhild von Amsberg
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Martini-Klinik, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon A Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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70
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Cristalli C, Scotlandi K. Targeting DNA Methylation Machinery in Pediatric Solid Tumors. Cells 2024; 13:1209. [PMID: 39056791 PMCID: PMC11275080 DOI: 10.3390/cells13141209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
DNA methylation is a key epigenetic regulatory mechanism that plays a critical role in a variety of cellular processes, including the regulation of cell fate during development, maintenance of cell identity, and genome stability. DNA methylation is tightly regulated by enzymatic reactions and its deregulation plays an important role in the development of cancer. Specific DNA methylation alterations have been found in pediatric solid tumors, providing new insights into the development of these tumors. In addition, DNA methylation profiles have greatly contributed to tune the diagnosis of pediatric solid tumors and to define subgroups of patients with different risks of progression, leading to the reduction in unwanted toxicity and the improvement of treatment efficacy. This review highlights the dysregulated DNA methylome in pediatric solid tumors and how this information provides promising targets for epigenetic therapies, particularly inhibitors of DNMT enzymes (DNMTis). Opportunities and limitations are considered, including the ability of DNMTis to induce viral mimicry and immune signaling by tumors. Besides intrinsic action against cancer cells, DNMTis have the potential to sensitize immune-cold tumors to immunotherapies and may represent a remarkable option to improve the treatment of challenging pediatric solid tumors.
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Affiliation(s)
- Camilla Cristalli
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
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Sievers P, Bielle F, Göbel K, Schrimpf D, Nichelli L, Mathon B, Appay R, Boldt HB, Dohmen H, Selignow C, Acker T, Vicha A, Martinetto H, Schweizer L, Schüller U, Brandner S, Wesseling P, Schmid S, Capper D, Abdullaev Z, Aldape K, Korshunov A, Krieg SM, Wick W, Pfister SM, von Deimling A, Reuss DE, Jones DTW, Sahm F. Identification of a putative molecular subtype of adult-type diffuse astrocytoma with recurrent MAPK pathway alterations. Acta Neuropathol 2024; 148:7. [PMID: 39026106 PMCID: PMC11258072 DOI: 10.1007/s00401-024-02766-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/18/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024]
Affiliation(s)
- Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
| | - Franck Bielle
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute, ICM, 75013, Paris, France
- Department of Neuropathology, AP-HP, Pitié-Salpêtrière Hospital, 75013, Paris, France
| | - Kirsten Göbel
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lucia Nichelli
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute, ICM, 75013, Paris, France
- Department of Neuroradiology, AP-HP, Pitié-Salpêtrière Hospital, 75013, Paris, France
| | - Bertrand Mathon
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute, ICM, 75013, Paris, France
- Department of Neurosurgery, AP-HP, Pitié-Salpêtrière Hospital, 75013, Paris, France
| | - Romain Appay
- Department of Pathology and Neuropathology, APHM, CHU Timone, Marseille, France
- Institute of Neurophysiopathol, CNRS, INP, Aix-Marseille University, Marseille, France
| | - Henning B Boldt
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Hildegard Dohmen
- Institute of Neuropathology, Justus-Liebig University Giessen, Giessen, Germany
| | - Carmen Selignow
- Institute of Neuropathology, Justus-Liebig University Giessen, Giessen, Germany
| | - Till Acker
- Institute of Neuropathology, Justus-Liebig University Giessen, Giessen, Germany
| | - Ales Vicha
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Horacio Martinetto
- Departamento de Neuropatología y Biología Molecular, Instituto de Investigaciones Neurológicas Dr Raúl Carrea (FLENI), Buenos Aires, Argentina
| | - Leonille Schweizer
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sebastian Brandner
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Pieter Wesseling
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, Amsterdam University Medical Centers, Location VUmc and Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Simone Schmid
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - David Capper
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Sandro M Krieg
- Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
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72
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Richardson TE, Walker JM, Hambardzumyan D, Brem S, Hatanpaa KJ, Viapiano MS, Pai B, Umphlett M, Becher OJ, Snuderl M, McBrayer SK, Abdullah KG, Tsankova NM. Genetic and epigenetic instability as an underlying driver of progression and aggressive behavior in IDH-mutant astrocytoma. Acta Neuropathol 2024; 148:5. [PMID: 39012509 PMCID: PMC11252228 DOI: 10.1007/s00401-024-02761-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/17/2024]
Abstract
In recent years, the classification of adult-type diffuse gliomas has undergone a revolution, wherein specific molecular features now represent defining diagnostic criteria of IDH-wild-type glioblastomas, IDH-mutant astrocytomas, and IDH-mutant 1p/19q-codeleted oligodendrogliomas. With the introduction of the 2021 WHO CNS classification, additional molecular alterations are now integrated into the grading of these tumors, given equal weight to traditional histologic features. However, there remains a great deal of heterogeneity in patient outcome even within these established tumor subclassifications that is unexplained by currently codified molecular alterations, particularly in the IDH-mutant astrocytoma category. There is also significant intercellular genetic and epigenetic heterogeneity and plasticity with resulting phenotypic heterogeneity, making these tumors remarkably adaptable and robust, and presenting a significant barrier to the design of effective therapeutics. Herein, we review the mechanisms and consequences of genetic and epigenetic instability, including chromosomal instability (CIN), microsatellite instability (MSI)/mismatch repair (MMR) deficits, and epigenetic instability, in the underlying biology, tumorigenesis, and progression of IDH-mutant astrocytomas. We also discuss the contribution of recent high-resolution transcriptomics studies toward defining tumor heterogeneity with single-cell resolution. While intratumoral heterogeneity is a well-known feature of diffuse gliomas, the contribution of these various processes has only recently been considered as a potential driver of tumor aggressiveness. CIN has an independent, adverse effect on patient survival, similar to the effect of histologic grade and homozygous CDKN2A deletion, while MMR mutation is only associated with poor overall survival in univariate analysis but is highly correlated with higher histologic/molecular grade and other aggressive features. These forms of genomic instability, which may significantly affect the natural progression of these tumors, response to therapy, and ultimately clinical outcome for patients, are potentially measurable features which could aid in diagnosis, grading, prognosis, and development of personalized therapeutics.
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Affiliation(s)
- Timothy E Richardson
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA.
| | - Jamie M Walker
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dolores Hambardzumyan
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
- Department of Neurosurgery, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kimmo J Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Mariano S Viapiano
- Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Neurosurgery, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Balagopal Pai
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melissa Umphlett
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
| | - Oren J Becher
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | - Samuel K McBrayer
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Nadejda M Tsankova
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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73
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Wu Z, Dazelle K, Abdullaev Z, Chung HJ, Dahiya S, Wood M, Lee H, Lucas CHG, Mao Q, Robinson L, Fernandes I, McCord M, Pytel P, Conway KS, Yoda R, Eschbacher JM, Maher OM, Hasselblatt M, Mobley BC, Raisanen JM, Hatanpaa KJ, Byers J, Lehman NL, Cimino PJ, Pratt D, Quezado M, Aldape K. Papillary tumor of the pineal region: analysis of DNA methylation profiles and clinical outcomes in 76 cases. Acta Neuropathol Commun 2024; 12:117. [PMID: 39014393 PMCID: PMC11251120 DOI: 10.1186/s40478-024-01781-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/13/2024] [Indexed: 07/18/2024] Open
Abstract
Papillary tumor of the pineal region (PTPR) is an uncommon tumor of the pineal region with distinctive histopathologic and molecular characteristics. Experience is limited with respect to its molecular heterogeneity and clinical characteristics. Here, we describe 39 new cases and combine these with 37 previously published cases for a cohort of 76 PTPR's, all confirmed by methylation profiling. As previously reported, two main methylation groups were identified (PTPR-A and PTPR-B). In our analysis we extended the subtyping into three subtypes: PTPR-A, PTPR-B1 and PTPR-B2 supported by DNA methylation profile and genomic copy number variations. Frequent loss of chromosome 3 or 14 was found in PTPR-B1 tumors but not in PTPR-B2. Examination of clinical outcome showed that nearly half (14/30, 47%) of examined patients experienced tumor progression with significant difference among the subtypes (p value = 0.046). Our analysis extends the understanding of this uncommon but distinct neuroepithelial tumor by describing its molecular heterogeneity and clinical outcomes, including its tendency towards tumor recurrence.
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Affiliation(s)
- Zhichao Wu
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Karen Dazelle
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Hye-Jung Chung
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Sonika Dahiya
- Division of Neuropathology, Washington University, St. Louis, MO, USA
| | - Matthew Wood
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Han Lee
- Neuropathology Division, Department of Pathology, University of California Davis, Sacramento, CA, USA
| | - Calixto-Hope G Lucas
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Qinwen Mao
- Department of Pathology, Primary Children's Hospital, Salt Lake City, UT, USA
| | - Lorraina Robinson
- Department of Pathology, Primary Children's Hospital, Salt Lake City, UT, USA
| | | | - Matthew McCord
- Department of Pathology, Northwestern Memorial Hospital, Chicago, IL, USA
| | - Peter Pytel
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Kyle S Conway
- Department of Pathology, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Rebecca Yoda
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Jennifer M Eschbacher
- Department of Neuropathology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, AZ, USA
| | - Ossama M Maher
- Division of Pediatric Neuro -Oncology, Pediatric Hematology and Oncology, Kidz Medical Services, Nicklaus Children's Hospital, Miami, FL, USA
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Bret C Mobley
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, USA
| | - Jack M Raisanen
- Division of Neuropathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kimmo J Hatanpaa
- Division of Neuropathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joshua Byers
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Norman L Lehman
- Department of Pathology, Baylor College of Medicine, Baylor Scott & White Medical Center, Temple, TX, USA
| | - Patrick J Cimino
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA.
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74
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Iijima K, Fujii H, Suzuki F, Murayama K, Goto YI, Saito Y, Sano T, Suzuki H, Miyata H, Kimura Y, Nakashima T, Suzuki H, Iwasaki M, Sato N. Genotype-relevant neuroimaging features in low-grade epilepsy-associated tumors. Front Neurol 2024; 15:1419104. [PMID: 39081340 PMCID: PMC11286587 DOI: 10.3389/fneur.2024.1419104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/12/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction Low-grade epilepsy-associated tumors are the second most common histopathological diagnoses in cases of drug-resistant focal epilepsy. However, the connection between neuroimaging features and genetic alterations in these tumors is unclear, prompting an investigation into genotype-relevant neuroimaging characteristics. Methods This study retrospectively analyzed neuroimaging and surgical specimens from 46 epilepsy patients with low-grade epilepsy-associated neuroepithelial tumors that had genetic mutations identified through panel sequencing to investigate their relationship to genotypes. Results Three distinct neuroimaging groups were established: Group 1 had indistinct borders and iso T1-weighted and slightly high or high T2-weighted signal intensities without a diffuse mass effect, associated with 93.8% sensitivity and 100% specificity to BRAF V600E mutations; Group 2 exhibited sharp borders and very or slightly low T1-weighted and very high T2-weighted signal intensities with a diffuse mass effect and 100% sensitivity and specificity for FGFR1 mutations; and Group 3 displayed various characteristics. Histopathological diagnoses including diffuse low-grade glioma and ganglioglioma showed no clear association with genotypes. Notably, postoperative seizure-free rates were higher in Group 1 tumors (BRAF V600E) than in Group 2 tumors (FGFR1). Discussion These findings suggest that tumor genotype may be predicted by neuroimaging before surgery, providing insights for personalized treatment approaches.
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Affiliation(s)
- Keiya Iijima
- Department of Neurosurgery, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Hiroyuki Fujii
- Department of Radiology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Fumio Suzuki
- Department of Radiology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Kumiko Murayama
- Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Yu-ichi Goto
- Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Yuko Saito
- Department of Pathology and Laboratory Medicine, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
- Department of Neurology, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan
| | - Terunori Sano
- Department of Pathology and Laboratory Medicine, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Hiroyoshi Suzuki
- Department of Pathology and Laboratory Medicine, National Hospital Organization Sendai Medical Center, Sendai, Miyagi, Japan
| | - Hajime Miyata
- Department of Neuropathology, Research Institute for Brain and Blood Vessels, Akita Cerebrospinal and Cardiovascular Center, Akita, Japan
| | - Yukio Kimura
- Department of Radiology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Takuma Nakashima
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiromichi Suzuki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Masaki Iwasaki
- Department of Neurosurgery, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Noriko Sato
- Department of Radiology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
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75
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Berzero G, Pieri V, Palazzo L, Finocchiaro G, Filippi M. Liquid biopsy in brain tumors: moving on, slowly. Curr Opin Oncol 2024:00001622-990000000-00195. [PMID: 39011725 DOI: 10.1097/cco.0000000000001079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
PURPOSE OF REVIEW Due to limited access to the tumor, there is an obvious clinical potential for liquid biopsy in patients with primary brain tumors. Here, we review current approaches, present limitations to be dealt with, and new promising data that may impact the field. RECENT FINDINGS The value of circulating tumor cell-free DNA (ctDNA) in the cerebrospinal fluid (CSF) for the noninvasive diagnosis of primary brain tumors has been confirmed in several reports. The detection of ctDNA in the peripheral blood is desirable for patient follow-up but requires ultrasensitive methods to identify low mutant allelic frequencies. Digital PCR approaches and targeted gene panels have been used to identify recurrent hotspot mutations and copy number variations (CNVs) from CSF or plasma. Tumor classification from circulating methylomes in plasma has been actively pursued, although the need of advanced bioinformatics currently hampers clinical application. The use of focused ultrasounds to open the blood-brain barrier may represent a way to enrich of ctDNA the peripheral blood and enhance plasma-based liquid biopsy. SUMMARY Monitoring CNVs and hotspot mutations by liquid biopsy is a promising tool to detect minimal residual disease and strengthen response assessment in patients with primary brain tumors. Novel methods to increase the relative and/or absolute amount of ctDNA can improve the clinical potential of plasma-based liquid biopsies.
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Affiliation(s)
- Giulia Berzero
- Neurology Unit, IRCCS Ospedale San Raffaele
- Vita-Salute San Raffaele University
| | - Valentina Pieri
- Neurology Unit, IRCCS Ospedale San Raffaele
- Vita-Salute San Raffaele University
| | - Leonardo Palazzo
- Neurology Unit, IRCCS Ospedale San Raffaele
- Vita-Salute San Raffaele University
| | | | - Massimo Filippi
- Neurology Unit, IRCCS Ospedale San Raffaele
- Vita-Salute San Raffaele University
- Neurorehabilitation Unit, Neurophysiology Unit, Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele, Milan, Italy
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76
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Geng Z, Wafula E, Corbett RJ, Zhang Y, Jin R, Gaonkar KS, Shukla S, Rathi KS, Hill D, Lahiri A, Miller DP, Sickler A, Keith K, Blackden C, Chroni A, Brown MA, Kraya AA, Koschmann CJ, Aldape K, Huang X, Rood BR, Mason JL, Trooskin GR, Abdullaev Z, Wang P, Zhu Y, Farrow BK, Farrel A, Dybas JM, Zhong C, Kuren NV, Zhang B, Santi M, Phul S, Chinwalla AT, Resnick AC, Diskin SJ, Tasian S, Stefankiewicz S, Maris JM, Ennis BM, Lueder MR, Naqvi AS, Coleman N, Ma W, Taylor D, Rokita JL. The Open Pediatric Cancer Project. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.599086. [PMID: 39026781 PMCID: PMC11257555 DOI: 10.1101/2024.07.09.599086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Background In 2019, the Open Pediatric Brain Tumor Atlas (OpenPBTA) was created as a global, collaborative open-science initiative to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Here, we extend the OpenPBTA to create the Open Pediatric Cancer (OpenPedCan) Project, a harmonized open-source multi-omic dataset from 6,112 pediatric cancer patients with 7,096 tumor events across more than 100 histologies. Combined with RNA-Seq from the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA), OpenPedCan contains nearly 48,000 total biospecimens (24,002 tumor and 23,893 normal specimens). Findings We utilized Gabriella Miller Kids First (GMKF) workflows to harmonize WGS, WXS, RNA-seq, and Targeted Sequencing datasets to include somatic SNVs, InDels, CNVs, SVs, RNA expression, fusions, and splice variants. We integrated summarized CPTAC whole cell proteomics and phospho-proteomics data, miRNA-Seq data, and have developed a methylation array harmonization workflow to include m-values, beta-vales, and copy number calls. OpenPedCan contains reproducible, dockerized workflows in GitHub, CAVATICA, and Amazon Web Services (AWS) to deliver harmonized and processed data from over 60 scalable modules which can be leveraged both locally and on AWS. The processed data are released in a versioned manner and accessible through CAVATICA or AWS S3 download (from GitHub), and queryable through PedcBioPortal and the NCI's pediatric Molecular Targets Platform. Notably, we have expanded PBTA molecular subtyping to include methylation information to align with the WHO 2021 Central Nervous System Tumor classifications, allowing us to create research- grade integrated diagnoses for these tumors. Conclusions OpenPedCan data and its reproducible analysis module framework are openly available and can be utilized and/or adapted by researchers to accelerate discovery, validation, and clinical translation.
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Affiliation(s)
- Zhuangzhuang Geng
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Eric Wafula
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Ryan J Corbett
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yuanchao Zhang
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Run Jin
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Krutika S Gaonkar
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sangeeta Shukla
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Komal S Rathi
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Dave Hill
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Aditya Lahiri
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Daniel P Miller
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Alex Sickler
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kelsey Keith
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Christopher Blackden
- Center for Data- Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Antonia Chroni
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Miguel A Brown
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Adam A Kraya
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Carl J Koschmann
- Department of Pediatrics, University of Michigan Health, Ann Arbor, MI, 48105, USA; Pediatric Hematology Oncology, Mott Children's Hospital, Ann Arbor, MI, 48109, USA
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Xiaoyan Huang
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Brian R Rood
- Children's National Research Institute, Washington, D.C.; George Washington University School of Medicine and Health Sciences, Washington, D.C., 20052, USA
| | - Jennifer L Mason
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Gerri R Trooskin
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Zied Abdullaev
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuankun Zhu
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Bailey K Farrow
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Alvin Farrel
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA · Funded by NCI/NIH Contract No. 75N91019D00024, Task Order No. 75N91020F00003
| | - Joseph M Dybas
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Chuwei Zhong
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Nicholas Van Kuren
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Bo Zhang
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Saksham Phul
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Asif T Chinwalla
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA · Funded by Children's Brain Tumor Network; NIH 3P30 CA016520- 44S5, U2C HL138346-03, U24 CA220457-03; NCI/NIH Contract No. 75N91019D00024, Task Order No. 75N91020F00003; Children's Hospital of Philadelphia Division of Neurosurgery
| | - Sharon J Diskin
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sarah Tasian
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephanie Stefankiewicz
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - John M Maris
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Brian M Ennis
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Matthew R Lueder
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Ammar S Naqvi
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Noel Coleman
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pediatrics, University of Pennsylvania Perelman Medical School, Philadelphia, PA, 19104, USA · Funded by NCI/NIH Contract No. 75N91019D00024, Task Order No. 75N91020F00003
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA · Funded by NCI/NIH Contract No. 75N91019D00024, Task Order No. 75N91020F00003
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Agaimy A, Stoehr R, Fisher C, Chrisinger JSA, Demicco EG, Tögel L, Michal M, Michal M. ALK-rearranged Mesenchymal Neoplasms With Prominent Foamy/Pseudolipogenic Cell Morphology: Expanding the Phenotypic Spectrum of ALK Fusion Neoplasms and Report of Novel Fusion Partners. Am J Surg Pathol 2024:00000478-990000000-00387. [PMID: 38979776 DOI: 10.1097/pas.0000000000002283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The category of ALK-rearranged mesenchymal neoplasms has been evolving rapidly, with reports of morphologically diverse lesions of cutaneous, soft tissue, and visceral origin. While some of these represent morphologically defined entities harboring recurrent ALK fusions (inflammatory myofibroblastic tumor and epithelioid fibrous histiocytoma), others are unclassified by morphology with variable overlap with the tyrosine kinase family of neoplasia and their underlying ALK fusions cannot be suspected based on morphology. We herein report 3 cases that expand the anatomic, morphologic, and genotypic spectrum of ALK-rearranged unclassified neoplasms. Patients were all adults aged 46 to 69 (median: 63) who presented with a mass located in the gingiva, subcutis of the back, and submucosal posterior pharyngeal wall. The tumor size ranged from 1 to 2.7 cm (median: 1.6). Conservative surgery was the treatment in all patients. Follow-up was available for one patient who remained disease-free at 14 months. Histologically, all tumors displayed large polygonal cells with foamy to granular and lipogenic-like microvacuolated copious cytoplasm and medium-sized round nuclei with 1 or 2 prominent nucleoli. Mitoses and necrosis were not seen. The initial diagnostic impression was PEComa, inflammatory rhabdomyoblastic tumor and unclassified pseudolipogenic neoplasm. Strong cytoplasmic ALK was detected by immunohistochemistry in all cases. Other positive markers include Cathepsin K (2/2), desmin (1/3), focal MyoD1 (1/1), focal SMA (1/3), and focal EMA (1/2). Targeted RNA sequencing revealed ALK fusions with exon 20 (2 cases) and exon 19 (one case) of ALK fused to RND3 (exon 3), SQSTM1 (exon 6), and desmin (intron 6). Methylation profiling in the desmin-fused case (initially diagnosed as inflammatory rhabdomyoblastic tumor) revealed an inflammatory myofibroblastic tumor match with a low confidence score of 0.5 and a flat copy number variation (CNV) profile. No NF1 mutation was detected in this case, altogether excluding an inflammatory rhabdomyoblastic tumor. Our study highlights and expands the morphologic and anatomic diversity of ALK-fused neoplasms and documents novel fusion partners (RND3 and desmin).
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Affiliation(s)
- Abbas Agaimy
- Institute of Pathology, Erlangen University Hospital, Friedrich Alexander University of Erlangen-Nuremberg
- Comprehensive Cancer Center, European Metropolitan Area Erlangen-Nuremberg (CCC ER-EMN), Erlangen, Germany
| | - Robert Stoehr
- Institute of Pathology, Erlangen University Hospital, Friedrich Alexander University of Erlangen-Nuremberg
- Comprehensive Cancer Center, European Metropolitan Area Erlangen-Nuremberg (CCC ER-EMN), Erlangen, Germany
| | - Cyril Fisher
- Department of Cellular Pathology, University Hospitals Birmingham, Birmingham, UK
| | - John S A Chrisinger
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Elizabeth G Demicco
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital and Laboratory Medicine and Pathobiology, University of Toronto, Canada
| | - Lars Tögel
- Institute of Pathology, Erlangen University Hospital, Friedrich Alexander University of Erlangen-Nuremberg
- Comprehensive Cancer Center, European Metropolitan Area Erlangen-Nuremberg (CCC ER-EMN), Erlangen, Germany
| | - Michal Michal
- Department of Pathology, Faculty of Medicine, Charles University, Plzen, Czech Republic
- Bioptical Laboratory, Ltd., Plzen, Czech Republic
| | - Michael Michal
- Department of Pathology, Faculty of Medicine, Charles University, Plzen, Czech Republic
- Bioptical Laboratory, Ltd., Plzen, Czech Republic
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78
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Wang YRJ, Wang P, Yan Z, Zhou Q, Gunturkun F, Li P, Hu Y, Wu WE, Zhao K, Zhang M, Lv H, Fu L, Jin J, Du Q, Wang H, Chen K, Qu L, Lin K, Iv M, Wang H, Sun X, Vogel H, Han S, Tian L, Wu F, Gong J. Advancing presurgical non-invasive molecular subgroup prediction in medulloblastoma using artificial intelligence and MRI signatures. Cancer Cell 2024; 42:1239-1257.e7. [PMID: 38942025 DOI: 10.1016/j.ccell.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/25/2024] [Accepted: 06/05/2024] [Indexed: 06/30/2024]
Abstract
Global investigation of medulloblastoma has been hindered by the widespread inaccessibility of molecular subgroup testing and paucity of data. To bridge this gap, we established an international molecularly characterized database encompassing 934 medulloblastoma patients from thirteen centers across China and the United States. We demonstrate how image-based machine learning strategies have the potential to create an alternative pathway for non-invasive, presurgical, and low-cost molecular subgroup prediction in the clinical management of medulloblastoma. Our robust validation strategies-including cross-validation, external validation, and consecutive validation-demonstrate the model's efficacy as a generalizable molecular diagnosis classifier. The detailed analysis of MRI characteristics replenishes the understanding of medulloblastoma through a nuanced radiographic lens. Additionally, comparisons between East Asia and North America subsets highlight critical management implications. We made this comprehensive dataset, which includes MRI signatures, clinicopathological features, treatment variables, and survival data, publicly available to advance global medulloblastoma research.
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Affiliation(s)
- Yan-Ran Joyce Wang
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; School of Medicine, Stanford University, Stanford, CA 94304, USA.
| | - Pengcheng Wang
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Zihan Yan
- Department of Pediatric Neurosurgery, Beijing Tiantan Hospital, Capital Medicine University, Beijing Neurosurgical Institute, Beijing 100070, China
| | - Quan Zhou
- School of Medicine, Stanford University, Stanford, CA 94304, USA; Department of Neurosurgery, Stanford School of Medicine, Stanford University, Stanford, CA 94304, USA
| | - Fatma Gunturkun
- School of Medicine, Stanford University, Stanford, CA 94304, USA; Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA 94304, USA
| | - Peng Li
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; School of Engineering, University of Science and Technology of China, Hefei 230001, China
| | - Yanshen Hu
- School of Engineering, University of Science and Technology of China, Hefei 230001, China
| | - Wei Emma Wu
- School of Medicine, Stanford University, Stanford, CA 94304, USA; Department of Radiology Oncology, Stanford University, Stanford, CA 94305, USA
| | - Kankan Zhao
- Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Michael Zhang
- School of Medicine, Stanford University, Stanford, CA 94304, USA; Department of Neurosurgery, Stanford School of Medicine, Stanford University, Stanford, CA 94304, USA
| | - Haoyi Lv
- School of Engineering, University of Science and Technology of China, Hefei 230001, China
| | - Lehao Fu
- School of Engineering, University of Science and Technology of China, Hefei 230001, China
| | - Jiajie Jin
- School of Engineering, University of Science and Technology of China, Hefei 230001, China
| | - Qing Du
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
| | - Haoyu Wang
- School of Engineering, University of Science and Technology of China, Hefei 230001, China
| | - Kun Chen
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Liangqiong Qu
- The Department of Statistics and Actuarial Science and the Institute of Data Science, The University of Hong Kong, Hong Kong 999077, China
| | - Keldon Lin
- Mayo Clinic Alix School of Medicine, Scottsdale, AZ 85054, USA
| | - Michael Iv
- School of Medicine, Stanford University, Stanford, CA 94304, USA; Department of Neurosurgery, Stanford School of Medicine, Stanford University, Stanford, CA 94304, USA
| | - Hao Wang
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; MoE Key Laboratory of Brain-inspired Intelligent Perception and Cognition, School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Xiaoyan Sun
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; School of Engineering, University of Science and Technology of China, Hefei 230001, China
| | - Hannes Vogel
- School of Medicine, Stanford University, Stanford, CA 94304, USA; Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, CA 94304, USA
| | - Summer Han
- School of Medicine, Stanford University, Stanford, CA 94304, USA; Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA 94304, USA
| | - Lu Tian
- School of Medicine, Stanford University, Stanford, CA 94304, USA; Department of Statistics, Stanford School of Medicine, Stanford University, Stanford, CA 94304, USA
| | - Feng Wu
- School of Engineering, University of Science and Technology of China, Hefei 230001, China
| | - Jian Gong
- Department of Pediatric Neurosurgery, Beijing Tiantan Hospital, Capital Medicine University, Beijing Neurosurgical Institute, Beijing 100070, China.
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79
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Cornelli L, Van Paemel R, Ferro Dos Santos MR, Roelandt S, Willems L, Vandersteene J, Baert E, Mus LM, Van Roy N, De Wilde B, De Preter K. Diagnosis of pediatric central nervous system tumors using methylation profiling of cfDNA from cerebrospinal fluid. Clin Epigenetics 2024; 16:87. [PMID: 38970137 PMCID: PMC11225235 DOI: 10.1186/s13148-024-01696-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/17/2024] [Indexed: 07/07/2024] Open
Abstract
Pediatric central nervous system tumors remain challenging to diagnose. Imaging approaches do not provide sufficient detail to discriminate between different tumor types, while the histopathological examination of tumor tissue shows high inter-observer variability. Recent studies have demonstrated the accurate classification of central nervous system tumors based on the DNA methylation profile of a tumor biopsy. However, a brain biopsy holds significant risk of bleeding and damaging the surrounding tissues. Liquid biopsy approaches analyzing circulating tumor DNA show high potential as an alternative and less invasive tool to study the DNA methylation pattern of tumors. Here, we explore the potential of classifying pediatric brain tumors based on methylation profiling of the circulating cell-free DNA (cfDNA) in cerebrospinal fluid (CSF). For this proof-of-concept study, we collected cerebrospinal fluid samples from 19 pediatric brain cancer patients via a ventricular drain placed for reasons of increased intracranial pressure. Analyses on the cfDNA showed high variability of cfDNA quantities across patients ranging from levels below the limit of quantification to 40 ng cfDNA per milliliter of CSF. Classification based on methylation profiling of cfDNA from CSF was correct for 7 out of 20 samples in our cohort. Accurate results were mostly observed in samples of high quality, more specifically those with limited high molecular weight DNA contamination. Interestingly, we show that centrifugation of the CSF prior to processing increases the fraction of fragmented cfDNA to high molecular weight DNA. In addition, classification was mostly correct for samples with high tumoral cfDNA fraction as estimated by computational deconvolution (> 40%). In summary, analysis of cfDNA in the CSF shows potential as a tool for diagnosing pediatric nervous system tumors especially in patients with high levels of tumoral cfDNA in the CSF. Further optimization of the collection procedure, experimental workflow and bioinformatic approach is required to also allow classification for patients with low tumoral fractions in the CSF.
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Affiliation(s)
- Lotte Cornelli
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Ruben Van Paemel
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Maísa R Ferro Dos Santos
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Sofie Roelandt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Leen Willems
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | | | - Edward Baert
- Department of Neurosurgery, Ghent University Hospital, Ghent, Belgium
| | - Liselot M Mus
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Nadine Van Roy
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Bram De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
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80
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Ricklefs FL, Wollmann K, Salviano-Silva A, Drexler R, Maire CL, Kaul MG, Reimer R, Schüller U, Heinemann S, Kolbe K, Mummert T, Glatzel M, Peine S, Gempt J, Westphal M, Dührsen L, Lamszus K. Circulating extracellular vesicles as biomarker for diagnosis, prognosis, and monitoring in glioblastoma patients. Neuro Oncol 2024; 26:1280-1291. [PMID: 38567448 PMCID: PMC11226867 DOI: 10.1093/neuonc/noae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Extracellular vesicles (EVs) obtained by noninvasive liquid biopsy from patient blood can serve as biomarkers. Here, we investigated the potential of circulating plasma EVs to serve as an indicator in the diagnosis, prognosis, and treatment response of glioblastoma patients. METHODS Plasma samples were collected from glioblastoma patients at multiple timepoints before and after surgery. EV concentrations were measured by nanoparticle tracking analysis and imaging flow cytometry. Tumor burden and edema were quantified by 3D reconstruction. EVs and tumors were further monitored in glioma-bearing mice. RESULTS Glioblastoma patients displayed a 5.5-fold increase in circulating EVs compared to healthy donors (P < .0001). Patients with higher EV levels had significantly shorter overall survival and progression-free survival than patients with lower levels, and the plasma EV concentration was an independent prognostic parameter for overall survival. EV levels correlated with the extent of peritumoral fluid-attenuated inversion recovery hyperintensity but not with the size of the contrast-enhancing tumor, and similar findings were obtained in mice. Postoperatively, EV concentrations decreased rapidly back to normal levels, and the magnitude of the decline was associated with the extent of tumor resection. EV levels remained low during stable disease, but increased again upon tumor recurrence. In some patients, EV resurgence preceded the magnetic resonance imaging detectability of tumor relapse. CONCLUSIONS Our findings suggest that leakiness of the blood-brain barrier may primarily be responsible for the high circulating EV concentrations in glioblastoma patients. Elevated EVs reflect tumor presence, and their quantification may thus be valuable in assessing disease activity.
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Affiliation(s)
- Franz L Ricklefs
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kathrin Wollmann
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Amanda Salviano-Silva
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Richard Drexler
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cecile L Maire
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael G Kaul
- Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rudolph Reimer
- Heinrich-Pette-Institut, Leibnitz Institute for Experimental Virology, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
- Department of Paediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sarina Heinemann
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Kolbe
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias Mummert
- Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Peine
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jens Gempt
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manfred Westphal
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lasse Dührsen
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Lamszus
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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81
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Tabouret E, Furtner J, Graillon T, Silvani A, Le Rhun E, Soffietti R, Lombardi G, Sepúlveda-Sánchez JM, Brandal P, Bendszus M, Golfinopoulos V, Gorlia T, Weller M, Sahm F, Wick W, Preusser M. 3D volume growth rate evaluation in the EORTC-BTG-1320 clinical trial for recurrent WHO grade 2 and 3 meningiomas. Neuro Oncol 2024; 26:1302-1309. [PMID: 38452246 PMCID: PMC11226865 DOI: 10.1093/neuonc/noae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND We previously reported that tumor 3D volume growth rate (3DVGR) classification could help in the assessment of drug activity in patients with meningioma using 3 main classes and a total of 5 subclasses: class 1: decrease; 2: stabilization or severe slowdown; 3: progression. The EORTC-BTG-1320 clinical trial was a randomized phase II trial evaluating the efficacy of trabectedin for recurrent WHO 2 or 3 meningioma. Our objective was to evaluate the discriminative value of 3DVGR classification in the EORTC-BTG-1320. METHODS All patients with at least 1 available MRI before trial inclusion were included. 3D volume was evaluated on consecutive MRI until progression. 2D imaging response was centrally assessed by MRI modified Macdonald criteria. Clinical benefit was defined as neurological or functional status improvement or steroid decrease or discontinuation. RESULTS Sixteen patients with a median age of 58.5 years were included. Best 3DVGR classes were: 1, 2A, 3A, and 3B in 2 (16.7%), 4 (33.3%), 2 (16.7%), and 4 (33.3%) patients, respectively. All patients with progression-free survival longer than 6 months had best 3DVGR class 1 or 2. 3DVGR classes 1 and 2 (combined) had a median overall survival of 34.7 months versus 7.2 months for class 3 (P = .061). All class 1 patients (2/2), 75% of class 2 patients (3/4), and only 10% of class 3 patients (1/10) had clinical benefit. CONCLUSIONS Tumor 3DVGR classification may be helpful to identify early signals of treatment activity in meningioma clinical trials.
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Affiliation(s)
- Emeline Tabouret
- Aix-Marseille Univ, APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service de Neurooncologie, Marseille, France
| | - Julia Furtner
- Faculty of Medicine and Dentistry, Research Center for Medical Image Analysis and Artificial Intelligence (MIAAI), Danube Private University, Krems, Austria
| | - Thomas Graillon
- Aix-Marseille Univ, APHM, CHU Timone, Service de Neuro-chirurgie, Marseille, France
| | - Antonio Silvani
- Department of Neuro-Oncology, IRCCS Fondazione Istituto Neurologico Carlo Besta, Milan, Italy
| | - Emilie Le Rhun
- Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | | | - Giuseppe Lombardi
- Department of Oncology, Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Juan Manuel Sepúlveda-Sánchez
- Hospital Universitario e Instituto de Investigación 12 de Octubre, Unidad Multidisciplinar de Neuro-Oncología, Madrid, Spain
| | - Petter Brandal
- Department of Oncology and Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | | | | | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Wick
- German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Matthias Preusser
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
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Xu H, Chen X, Sun Y, Hu X, Zhang X, Wang Y, Tang Q, Zhu Q, Song K, Chen H, Sheng X, Yao Y, Zhuang D, Chen L, Mao Y, Qin Z. Comprehensive molecular characterization of long-term glioblastoma survivors. Cancer Lett 2024; 593:216938. [PMID: 38734160 DOI: 10.1016/j.canlet.2024.216938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
Fewer than 5 % glioblastoma (GBM) patients survive over five years and are termed long-term survivors (LTS), yet their molecular background is unclear. The present cohort included 72 isocitrate dehydrogenase (IDH)-wildtype GBM patients, consisting of 35 LTS and 37 short-term survivors (STS), and we employed whole exome sequencing, RNA-seq and DNA methylation array to delineate this largest LTS cohort to date. Although LTS and STS demonstrated analogous clinical characters and classical GBM biomarkers, CASC5 (P = 0.002) and SPEN (P = 0.013) mutations were enriched in LTS, whereas gene-to-gene fusions were concentrated in STS (P = 0.007). Importantly, LTS exhibited higher tumor mutation burden (P < 0.001) and copy number (CN) increase (P = 0.013), but lower mutant-allele tumor heterogeneity score (P < 0.001) and CN decrease (P = 0.026). Additionally, LTS demonstrated hypermethylated genome (P < 0.001) relative to STS. Differentially expressed and methylated genes both enriched in olfactory transduction. Further, analysis of the tumor microenvironment revealed higher infiltration of M1 macrophages (P = 0.043), B cells (P = 0.016), class-switched memory B cells (P = 0.002), central memory CD4+ T cells (P = 0.031) and CD4+ Th1 cells (P = 0.005) in LTS. We also separately analyzed a subset of patients who were methylation class-defined GBM, contributing 70.8 % of the entire cohort, and obtained similar results relative to prior analyses. Finally, we demonstrated that LTS and STS could be distinguished using a subset of molecular features. Taken together, the present study delineated unique molecular attributes of LTS GBM.
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Affiliation(s)
- Hao Xu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Xinyu Chen
- Department of Breast and Urologic Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ying Sun
- GenomiCare Biotechnology (Shanghai) Co. Ltd., Shanghai, China; Department of Data Science, Shanghai CreateCured Biotechnology Co. Ltd., Shanghai, China
| | - Xiaomu Hu
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xuan Zhang
- GenomiCare Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Ye Wang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Qisheng Tang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Qiongji Zhu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Kun Song
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaofang Sheng
- Department of Radiation Oncology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yu Yao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Dongxiao Zhuang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Lingchao Chen
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China.
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China.
| | - Zhiyong Qin
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China.
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Ng DP, Simonson PD, Tarnok A, Lucas F, Kern W, Rolf N, Bogdanoski G, Green C, Brinkman RR, Czechowska K. Recommendations for using artificial intelligence in clinical flow cytometry. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2024; 106:228-238. [PMID: 38407537 DOI: 10.1002/cyto.b.22166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 01/16/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024]
Abstract
Flow cytometry is a key clinical tool in the diagnosis of many hematologic malignancies and traditionally requires close inspection of digital data by hematopathologists with expert domain knowledge. Advances in artificial intelligence (AI) are transferable to flow cytometry and have the potential to improve efficiency and prioritization of cases, reduce errors, and highlight fundamental, previously unrecognized associations with underlying biological processes. As a multidisciplinary group of stakeholders, we review a range of critical considerations for appropriately applying AI to clinical flow cytometry, including use case identification, low and high risk use cases, validation, revalidation, computational considerations, and the present regulatory frameworks surrounding AI in clinical medicine. In particular, we provide practical guidance for the development, implementation, and suggestions for potential regulation of AI-based methods in the clinical flow cytometry laboratory. We expect these recommendations to be a helpful initial framework of reference, which will also require additional updates as the field matures.
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Affiliation(s)
- David P Ng
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Paul D Simonson
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Attila Tarnok
- Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, IZI, Leipzig, Germany
| | - Fabienne Lucas
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory GmbH, Munich, Germany
| | - Nina Rolf
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Goce Bogdanoski
- Clinical Development & Operations Quality, R&D Quality, Bristol Myers Squibb, Princeton, New Jersey, USA
| | - Cherie Green
- Translational Science, Ozette Technologies, Seattle, Washington, USA
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84
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Alturkustani M. Unraveling morphology, methylation profiling, and diagnostic challenges in BRAF-Mutant pediatric glial and glioneuronal tumors. NEUROSCIENCES (RIYADH, SAUDI ARABIA) 2024; 29:168-176. [PMID: 38981632 PMCID: PMC11305341 DOI: 10.17712/nsj.2024.3.20230108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/09/2024] [Indexed: 07/11/2024]
Abstract
OBJECTIVES To elucidate the relationship between DNA methylation profiling (DMP) and pathological diagnosis (PD) in pediatric glial and glioneuronal tumors with B-Raf proto-oncogene, serine/threonine kinase (BRAF) mutations, addressing their diagnostic challenges. METHODS This retrospective study, conducted in Saudi Arabia, analyzed 47 cases from the Children's Brain Tumor Network online database using scanned images, next-generation sequencing data, and methylation profiles processed using the Heidelberg methylation brain tumor classifiers v12.5 and v12.8. The data was last access on 10 November 2023. RESULTS The highest prevalence of BRAF mutations was observed in pilocytic astrocytoma and ganglioglioma. The DMP was consistent with PD in 23 cases, but discrepancies emerged in others, including diagnostic changes in diffuse leptomeningeal glioneuronal tumor and polymorphous low-grade neuroepithelial tumor of the young. A key inconsistency appeared between a pilocytic astrocytoma MC and a glioneuronal tumor PD. Two high-grade astrocytomas were misclassified as pleomorphic xanthoastrocytomas. Additionally, low variant allelic frequency in gangliogliomas likely contributed to misclassifications as control in 5 cases. CONCLUSION This study emphasized the importance of integrating DMP with PD in diagnosing pediatric glial and glioneuronal tumors with BRAF mutations. Although DMP offers significant diagnostic insights, its limitations, particularly in cases with low tumor content, necessitate cautious interpretation, as well as its use as a complementary diagnostic tool, rather than a definitive method.
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Affiliation(s)
- Murad Alturkustani
- From the Department of Pathology, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia, and from the Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
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85
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Rizvi T, Hussein MZ, Quezado M, Fadul CE, Lopes B. Atypical Choroid Plexus Tumor of the Cauda Equina With Metastases to the Spinal Cord and Brain. Cureus 2024; 16:e64947. [PMID: 39161498 PMCID: PMC11330702 DOI: 10.7759/cureus.64947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2024] [Indexed: 08/21/2024] Open
Abstract
We report a case of a 57-year-old man with a tumor arising from the cauda equina with spinal cord and intracranial metastases in the basal cisterns and along the cranial nerves. He presented with severe lower back pain and mild gait imbalance. His imaging revealed a large mass in the lumbosacral region with involvement of the cauda equina, intradural extramedullary enhancing metastases in the thoracic spinal canal, and intracranial metastases in the suprasellar cistern and along both trigeminal and facial/vestibulocochlear nerve complexes. Pathological examination of the resected thoracic spinal cord mass showed an atypical papillary proliferation with moderate nuclear pleomorphism and rare mitotic figures. While the morphologic and immunophenotypic features were consistent with the diagnosis of a choroid plexus tumor, the atypical location for this entity required the exclusion of other epithelioid tumors with papillary architecture. Additional immunohistochemical markers were used to exclude a metastatic adenocarcinoma, a papillary variant of a meningioma, and a papillary variant of an ependymoma. Ultimately, methylation-based tumor profiling determined that the methylation class was a match for "plexus tumor" resulting in the integrated diagnosis of the tumor with features of choroid plexus papilloma. This is a unique presentation for both the location and the metastatic spread. The methylation profile was instrumental in establishing this diagnosis.
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Affiliation(s)
- Tanvir Rizvi
- Radiology and Medical Imaging, University of Virginia School of Medicine, Charlottesville, USA
| | - Mohamed Z Hussein
- Diagnostic Radiology and Nuclear Medicine, Rush University Medical Center, Chicago, USA
| | | | - Camilo E Fadul
- Neuro-Oncology, University of Virginia School of Medicine, Charlottesville, USA
| | - Beatriz Lopes
- Neuropathology, University of Virginia School of Medicine, Charlottesville, USA
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86
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Mangum R, Lin FY, Parsons DW. Recent Advancements and Innovations in Pediatric Precision Oncology. J Pediatr Hematol Oncol 2024; 46:262-271. [PMID: 38857189 DOI: 10.1097/mph.0000000000002871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 03/29/2024] [Indexed: 06/12/2024]
Abstract
Precision oncology incorporates comprehensive genomic profiling into the individualized clinical care of pediatric cancer patients. In recent years, comprehensive pan-cancer analyses have led to the successful implementation of genomics-based pediatric trials and accelerated approval of novel targeted agents. In addition, disease-specific studies have resulted in molecular subclassification of myriad cancer types with subsequent tailoring of treatment intensity based on the patient's prognostic factors. This review discusses the progress of the field and highlights developments that are leading to more personalized cancer care and improved patient outcomes. Increased understanding of the evolution of precision oncology over recent decades emphasizes the tremendous impact of improved genomic applications. New technologies and improved diagnostic modalities offer further promise for future advancements within the field.
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Affiliation(s)
- Ross Mangum
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, AZ
| | - Frank Y Lin
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
| | - D Williams Parsons
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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87
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Chen BH, Zhou W. mLiftOver: harmonizing data across Infinium DNA methylation platforms. Bioinformatics 2024; 40:btae423. [PMID: 38963309 PMCID: PMC11233119 DOI: 10.1093/bioinformatics/btae423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/07/2024] [Accepted: 07/03/2024] [Indexed: 07/05/2024] Open
Abstract
MOTIVATION Infinium DNA methylation BeadChips are widely used for genome-wide DNA methylation profiling at the population scale. Recent updates to probe content and naming conventions in the EPIC version 2 (EPICv2) arrays have complicated integrating new data with previous Infinium array platforms, such as the MethylationEPIC (EPIC) and the HumanMethylation450 (HM450) BeadChip. RESULTS We present mLiftOver, a user-friendly tool that harmonizes probe ID, methylation level, and signal intensity data across different Infinium platforms. It manages probe replicates, missing data imputation, and platform-specific bias for accurate data conversion. We validated the tool by applying HM450-based cancer classifiers to EPICv2 cancer data, achieving high accuracy. Additionally, we successfully integrated EPICv2 healthy tissue data with legacy HM450 data for tissue identity analysis and produced consistent copy number profiles in cancer cells. AVAILABILITY AND IMPLEMENTATION mLiftOver is implemented R and available in the Bioconductor package SeSAMe (version 1.21.13+): https://bioconductor.org/packages/release/bioc/html/sesame.html. Analysis of EPIC and EPICv2 platform-specific bias and high-confidence mapping is available at https://github.com/zhou-lab/InfiniumAnnotationV1/raw/main/Anno/EPICv2/EPICv2ToEPIC_conversion.tsv.gz. The source code is available at https://github.com/zwdzwd/sesame/blob/devel/R/mLiftOver.R under the MIT license.
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Affiliation(s)
- Brian H Chen
- California Pacific Medical Center Research Institute, Sutter Health, San Francisco, CA 94143, United States
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, United States
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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88
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Hoang DT, Shulman ED, Turakulov R, Abdullaev Z, Singh O, Campagnolo EM, Lalchungnunga H, Stone EA, Nasrallah MP, Ruppin E, Aldape K. Prediction of DNA methylation-based tumor types from histopathology in central nervous system tumors with deep learning. Nat Med 2024; 30:1952-1961. [PMID: 38760587 DOI: 10.1038/s41591-024-02995-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 04/11/2024] [Indexed: 05/19/2024]
Abstract
Precision in the diagnosis of diverse central nervous system (CNS) tumor types is crucial for optimal treatment. DNA methylation profiles, which capture the methylation status of thousands of individual CpG sites, are state-of-the-art data-driven means to enhance diagnostic accuracy but are also time consuming and not widely available. Here, to address these limitations, we developed Deep lEarning from histoPathoLOgy and methYlation (DEPLOY), a deep learning model that classifies CNS tumors to ten major categories from histopathology. DEPLOY integrates three distinct components: the first classifies CNS tumors directly from slide images ('direct model'), the second initially generates predictions for DNA methylation beta values, which are subsequently used for tumor classification ('indirect model'), and the third classifies tumor types directly from routinely available patient demographics. First, we find that DEPLOY accurately predicts beta values from histopathology images. Second, using a ten-class model trained on an internal dataset of 1,796 patients, we predict the tumor categories in three independent external test datasets including 2,156 patients, achieving an overall accuracy of 95% and balanced accuracy of 91% on samples that are predicted with high confidence. These results showcase the potential future use of DEPLOY to assist pathologists in diagnosing CNS tumors within a clinically relevant short time frame.
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Affiliation(s)
- Danh-Tai Hoang
- Biological Data Science Institute, College of Science, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eldad D Shulman
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Rust Turakulov
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Omkar Singh
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Emma M Campagnolo
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - H Lalchungnunga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Eric A Stone
- Biological Data Science Institute, College of Science, Australian National University, Canberra, Australian Capital Territory, Australia
| | - MacLean P Nasrallah
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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Minasi S, Gianno F, Bargiacchi L, Barresi V, Miele E, Antonelli M, Buttarelli FR. Case report of a pediatric medulloblastoma with concurrent MYC and MYCN subclonal amplification in distinct populations of neoplastic cells. Virchows Arch 2024; 485:153-158. [PMID: 37212894 DOI: 10.1007/s00428-023-03560-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/17/2023] [Accepted: 05/10/2023] [Indexed: 05/23/2023]
Abstract
Medulloblastomas (MDBs) are classified into molecular groups showing peculiar immunohistochemical and genetic features and distinct DNA methylation profile. Group 3 and group 4 MDBs have the worst prognosis; the former is treated with high-risk protocols and features MYC amplification, whereas the latter receives standard-risk protocols and harbors MYCN amplification. Herein, we report a unique case of MDB showing histological and immunohistochemical features consistent with non-SHH/non-WNT classic MDB, with both MYCN (30% of tumor cells) and MYC (5-10% tumor cells) amplification in distinct subclones of neoplastic cells at fluorescence in situ hybridization (FISH), characterized by specific patterns. In spite of MYC amplification in only a small percentage of tumor cells, this case had DNA methylation profile consistent with group 3, emphasizing the importance to test both MYC and MYCN amplifications at a single cell level using highly sensitive methods, such as FISH, for diagnostic and therapeutic purposes.
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Affiliation(s)
- Simone Minasi
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, "Sapienza" University of Rome, Viale Regina Elena, 324-00161, Rome, Italy.
| | - Francesca Gianno
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, "Sapienza" University of Rome, Viale Regina Elena, 324-00161, Rome, Italy
| | - Lavinia Bargiacchi
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, "Sapienza" University of Rome, Viale Regina Elena, 324-00161, Rome, Italy
| | - Valeria Barresi
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Evelina Miele
- Department of Oncology/Hematology, Gene and Cell Therapy and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manila Antonelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, "Sapienza" University of Rome, Viale Regina Elena, 324-00161, Rome, Italy
| | - Francesca Romana Buttarelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, "Sapienza" University of Rome, Viale Regina Elena, 324-00161, Rome, Italy
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Ono T, Suzuki H, Nanjo H, Shimizu H. Clinical Course after Carmustine Wafer Implantation for Newly Diagnosed Adult-type Diffuse Gliomas; A controlled propensity matched analysis of a single center cohort. J Neurooncol 2024; 168:393-404. [PMID: 38780714 DOI: 10.1007/s11060-024-04679-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
PURPOSE It remains unclear whether combining carmustine wafer (CW) implantation with the standard treatment for adult-type diffuse gliomas is safe and has a prognostic impact. This study aimed to investigate the prognostic value and safety of CW implantation. METHODS Adult patients with IDH-wild-type and -mutant gliomas, grades 3-4 treated with surgical resection, radiotherapy, and temozolomide chemotherapy between 2013 and 2023 were surveyed. CWs were implanted except in cases of intraoperative wide ventricle opening or marked preoperative brain swelling. For survival analyses, a case-matched dataset based on propensity score matching (PSM), including multiple factors (patient background, diagnosis, and extent of resection) was generated. Progression-free survival (PFS), overall survival (OS), and frequency of complications of CW implantation (brain edema, infection, and cerebrospinal fluid leakage) were compared between the CW and non-use groups. RESULTS In total, 127 patients (75 in the CW use group and 52 in the non-use group) were enrolled. Regardless of stratification, no significant differences in PFS and OS were observed between the CW use and non-use groups. The frequency of postoperative brain edema was significantly higher in the CW use group than in the non-use group. An adjusted dataset containing 41 patients in the CW use and nonuse groups was generated. Even after PSM, CW implantation had no prognostic effect. CONCLUSIONS CW implantation with standard treatment demonstrated little beneficial effect for the present strategy of CW use.
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Affiliation(s)
- Takahiro Ono
- Department of Neurosurgery, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita, Akita, 010-8543, Japan.
| | - Hayato Suzuki
- Department of Neurosurgery, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita, Akita, 010-8543, Japan
| | - Hiroshi Nanjo
- Department of Surgical Pathology, Akita University Hospital, 44-2 Hasunuma Hiroomote, Akita, Akita, 010-8543, Japan
| | - Hiroaki Shimizu
- Department of Neurosurgery, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita, Akita, 010-8543, Japan
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Chien F, Michaud ME, Bakhtiari M, Schroff C, Snuderl M, Velazquez Vega JE, MacDonald TJ, Bhasin MK. Medulloblastoma Spatial Transcriptomics Reveals Tumor Microenvironment Heterogeneity with High-Density Progenitor Cell Regions Correlating with High-Risk Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600684. [PMID: 38979174 PMCID: PMC11230370 DOI: 10.1101/2024.06.25.600684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The tumor microenvironment (TME) of medulloblastoma (MB) influences progression and therapy response, presenting a promising target for therapeutic advances. Prior single-cell analyses have characterized the cellular components of the TME but lack spatial context. To address this, we performed spatial transcriptomic sequencing on sixteen pediatric MB samples obtained at diagnosis, including two matched diagnosis-relapse pairs. Our analyses revealed inter- and intra-tumoral heterogeneity within the TME, comprised of tumor-associated astrocytes (TAAs), macrophages (TAMs), stromal components, and distinct subpopulations of MB cells at different stages of neuronal differentiation and cell cycle progression. We identified dense regions of quiescent progenitor-like MB cells enriched in patients with high-risk (HR) features and an increase in TAAs, TAMs, and dysregulated vascular endothelium following relapse. Our study presents novel insights into the spatial architecture and cellular landscape of the medulloblastoma TME, highlighting spatial patterns linked to HR features and relapse, which may serve as potential therapeutic targets.
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Affiliation(s)
- Franklin Chien
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, GA 30322, USA
| | - Marina E. Michaud
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Mojtaba Bakhtiari
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Chanel Schroff
- Department of Pathology, NYU Langone Health and Grossman School of Medicine, New York, NY 10016, USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health and Grossman School of Medicine, New York, NY 10016, USA
| | - Jose E. Velazquez Vega
- Department of Pathology and Laboratory Medicine, Children’s Healthcare of Atlanta and Emory School of Medicine, Atlanta, GA 30322, USA
| | - Tobey J. MacDonald
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, GA 30322, USA
| | - Manoj K. Bhasin
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, GA 30322, USA
- Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
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92
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Hou Y, Du Y, Wang J, Zhang X, Zhao X, Xian X, Yuan L, Li H, Wang Y, Xi S, Huang G, Zhu W, Wang J, Zhu J, Yu Q, Cao Y, Wu J, Zeng J, Dong G, Hu W. Pediatric central nervous system tumor with CIC::LEUTX fusion: a diagnostic challenge. Acta Neuropathol Commun 2024; 12:106. [PMID: 38926750 PMCID: PMC11210039 DOI: 10.1186/s40478-024-01824-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024] Open
Affiliation(s)
- Yanghao Hou
- Department of Pathology, Center for Molecular Medicine Testing, College of Basic Medicine, Chongqing Medical University, Chongqing, P. R. China
| | - Yanru Du
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, P. R. China
| | - Juan Wang
- Department of Pathology, Nanjing Brain Hospital, Nanjing, P. R. China
| | - Xinke Zhang
- Department of Pathology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Xueyan Zhao
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
| | - Xinyi Xian
- Department of Pathology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Li Yuan
- Department of Pathology, Guangzhou Women and Children Medical Center, Guangzhou, P. R. China
| | - Haigang Li
- Department of Pathology, Sun Yat-sen Memorial Hospital, Guangzhou, P. R. China
| | - Yu Wang
- Department of Pathology, Zhujiang Hospital of Southern Medical University, Zhujiang, P. R. China
| | - Shaoyan Xi
- Department of Pathology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Guan Huang
- Department of Pathology, Longgang District Central Hospital of Shenzhen, Shenzhen, P. R. China
| | - Wenbiao Zhu
- Department of Pathology, Meizhou People's Hospital, Meizhou, P. R. China
| | - Juan Wang
- Department of Pediatric tumor, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Jin Zhu
- Department of Pathology, Center for Molecular Medicine Testing, College of Basic Medicine, Chongqing Medical University, Chongqing, P. R. China
- Department of Pathology, Children's hospital of Chongqing medical university, Chongqing, P. R. China
| | - Qiubo Yu
- Department of Pathology, Center for Molecular Medicine Testing, College of Basic Medicine, Chongqing Medical University, Chongqing, P. R. China
| | - Youde Cao
- Department of Pathology, Center for Molecular Medicine Testing, College of Basic Medicine, Chongqing Medical University, Chongqing, P. R. China
| | - JingXian Wu
- Department of Pathology, Center for Molecular Medicine Testing, College of Basic Medicine, Chongqing Medical University, Chongqing, P. R. China
| | - Jing Zeng
- Department of Pathology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.
| | - Gehong Dong
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, P. R. China.
| | - Wanming Hu
- Department of Pathology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.
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93
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van den Bent MJ, French PJ, Brat D, Tonn JC, Touat M, Ellingson BM, Young RJ, Pallud J, von Deimling A, Sahm F, Figarella Branger D, Huang RY, Weller M, Mellinghoff IK, Cloughsey TF, Huse JT, Aldape K, Reifenberger G, Youssef G, Karschnia P, Noushmehr H, Peters KB, Ducray F, Preusser M, Wen PY. The biological significance of tumor grade, age, enhancement and extent of resection in IDH mutant gliomas: how should they inform treatment decision in the era of IDH inhibitors? Invited review. Neuro Oncol 2024:noae107. [PMID: 38912846 DOI: 10.1093/neuonc/noae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Indexed: 06/25/2024] Open
Abstract
The 2016 and 2021 World Health Organization (WHO) 2021 Classification of Central Nervous System (CNS) tumors have resulted in a major improvement of the classification of IDH-mutant gliomas. With more effective treatments many patients experience prolonged survival . However, treatment guidelines are often still based on information from historical series comprising both patients with IDHwt and IDH mutant tumors. They provide recommendations for radiotherapy and chemotherapy for so-called high-risk patients, usually based on residual tumor after surgery and age over 40. More up-to-date studies give a better insight into clinical, radiological and molecular factors associated with outcome of patients with IDH-mutant glioma. These insights should be used today for risk stratification and for treatment decisions. In many patients with an IDH-mutant grade 2 and grade 3 glioma, if carefully monitored postponing radiotherapy and chemotherapy is safe, and will not jeopardize overall outcome of patients. With the INDIGO trial showing patient benefit from the IDH inhibitor vorasidenib, there is a sizable population in which it seems reasonable to try this class of agents before recommending radio-chemotherapy with its delayed adverse event profile affecting quality of survival. Ongoing trials should help to further identify the patients that are benefiting from this treatment.
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Affiliation(s)
| | - Pim J French
- Brain Tumor Center at ErasmusMC Cancer Institute, Rotterdam, the Netherlands
| | - Daniel Brat
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Joerg C Tonn
- Department of Neurosurgery, Ludwig-Maximilians-University, Munich, Germany and German Cancer Consortium (DKTK), Partner Site Munich, Germany
| | - Mehdi Touat
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau, Paris Brain Institute, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Benjamin M Ellingson
- UCLA Brain Tumor Imaging Laboratory, Department of Radiological Sciences, David Geffen School of Medicine at UCLA
| | - Robert J Young
- Neuroradiology Service, Department of Radiology, Memorial Sloan Kettering Cancer, New York, NY USA
| | - Johan Pallud
- Service de Neurochirurgie, GHU-Paris Psychiatrie et Neurosciences, Site Sainte Anne, F-75014 Paris, France
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, IMA-Brain, F-75014 Paris, France
| | - Andreas von Deimling
- Dept. of Neuropathology, University Hospital Medicine and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Dept. of Neuropathology, University Hospital Medicine and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominique Figarella Branger
- DFB Aix-Marseille Univ, APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Marseille, France
| | - Raymond Y Huang
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA USA
| | - Michael Weller
- Department of Neurology & Brain Tumor Center, University Hospital Zurich & University of Zurich, Zurich, Switzerland
| | - Ingo K Mellinghoff
- Department of Neurology, Memorial Sloan Kettering Cancer Center, 1275 York Ave., New York, NY
| | - Tim F Cloughsey
- TC David Geffen School of Medicine at UCLA, Department of Neurology
| | - Jason T Huse
- Department of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenneth Aldape
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Guido Reifenberger
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University and University Hospital Düsseldorf, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Gilbert Youssef
- Center For Neuro-Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Philipp Karschnia
- Department of Neurosurgery, Ludwig-Maximilians-University, Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich, Germany
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Hospital+Michigan State University, Detroit, Michigan, USA
| | - Katherine B Peters
- Department of Neurosurgery, Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC, USA
| | - Francois Ducray
- Hospices Civils de Lyon, Service de neuro-oncologie, LabEx Dev2CAN, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université Claude Bernard Lyon, Lyon, France
| | - Matthias Preusser
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Patrick Y Wen
- Center For Neuro-Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
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94
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Weller J, Potthoff AL, Zeyen T, Schaub C, Duffy C, Schneider M, Herrlinger U. Current status of precision oncology in adult glioblastoma. Mol Oncol 2024. [PMID: 38899374 DOI: 10.1002/1878-0261.13678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/05/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The concept of precision oncology, the application of targeted drugs based on comprehensive molecular profiling, has revolutionized treatment strategies in oncology. This review summarizes the current status of precision oncology in glioblastoma (GBM), the most common and aggressive primary brain tumor in adults with a median survival below 2 years. Targeted treatments without prior target verification have consistently failed. Patients with BRAF V600E-mutated GBM benefit from BRAF/MEK-inhibition, whereas targeting EGFR alterations was unsuccessful due to poor tumor penetration, tumor cell heterogeneity, and pathway redundancies. Systematic screening for actionable molecular alterations resulted in low rates (< 10%) of targeted treatments. Efficacy was observed in one-third and currently appears to be limited to BRAF-, VEGFR-, and mTOR-directed treatments. Advancing precision oncology for GBM requires consideration of pathways instead of single alterations, new trial concepts enabling rapid and adaptive drug evaluation, a focus on drugs with sufficient bioavailability in the CNS, and the extension of target discovery and validation to the tumor microenvironment, tumor cell networks, and their interaction with immune cells and neurons.
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Affiliation(s)
- Johannes Weller
- Department of Neurooncology, Center for Neurology, University Hospital Bonn, Germany
| | | | - Thomas Zeyen
- Department of Neurooncology, Center for Neurology, University Hospital Bonn, Germany
| | - Christina Schaub
- Department of Neurooncology, Center for Neurology, University Hospital Bonn, Germany
| | - Cathrina Duffy
- Department of Neurooncology, Center for Neurology, University Hospital Bonn, Germany
| | | | - Ulrich Herrlinger
- Department of Neurooncology, Center for Neurology, University Hospital Bonn, Germany
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95
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Parker M, Kazemi F, Krishnakumar A, Horowitz MA, Myneni S, Liu A, Schreck KC, Lucas CHG, Mukherjee D. Availability and utilization of molecular testing for primary central nervous system tumors among US hospitals. J Neuropathol Exp Neurol 2024; 83:579-585. [PMID: 38687613 PMCID: PMC11187421 DOI: 10.1093/jnen/nlae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Abstract
Advanced molecular testing has increasingly become an integral component for accurate diagnosis of central nervous system (CNS) tumors. We sought to establish the current state of molecular testing availability and approaches for the diagnosis of CNS tumors in US hospitals that conduct high volumes of CNS tumor resections. We distributed a 16-item survey inquiring about molecular testing approaches for CNS tumors to 115 neuropathologists at US hospitals with neurosurgery residency programs. Thirty-five neuropathologists (30.4%) responded to the survey, all of whom indicated their institutions perform molecular testing on CNS tumor tissue. The most commonly offered tests were MGMT methylation profiling and next-generation sequencing. Fourteen respondents (40%) indicated that their institution is able to test for and report all of the molecular alterations included in our survey. Nine (25.7%) respondents indicated that molecular testing is performed as standard of care for all patients with resected CNS tumors. Our results suggest that even in academic hospitals with a high volume of CNS tumor resections, molecular testing for these tumors is limited. Continued initiatives are necessary to expand the availability of molecular testing for CNS tumors to ensure diagnostic accuracy and guide targeted therapy.
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Affiliation(s)
- Megan Parker
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Foad Kazemi
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Asha Krishnakumar
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Melanie A Horowitz
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Saket Myneni
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Abby Liu
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Karisa C Schreck
- Department of Neurology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Calixto-Hope G Lucas
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Debraj Mukherjee
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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96
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Newsham I, Sendera M, Jammula SG, Samarajiwa SA. Early detection and diagnosis of cancer with interpretable machine learning to uncover cancer-specific DNA methylation patterns. Biol Methods Protoc 2024; 9:bpae028. [PMID: 38903861 PMCID: PMC11186673 DOI: 10.1093/biomethods/bpae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/30/2024] [Accepted: 04/29/2024] [Indexed: 06/22/2024] Open
Abstract
Cancer, a collection of more than two hundred different diseases, remains a leading cause of morbidity and mortality worldwide. Usually detected at the advanced stages of disease, metastatic cancer accounts for 90% of cancer-associated deaths. Therefore, the early detection of cancer, combined with current therapies, would have a significant impact on survival and treatment of various cancer types. Epigenetic changes such as DNA methylation are some of the early events underlying carcinogenesis. Here, we report on an interpretable machine learning model that can classify 13 cancer types as well as non-cancer tissue samples using only DNA methylome data, with 98.2% accuracy. We utilize the features identified by this model to develop EMethylNET, a robust model consisting of an XGBoost model that provides information to a deep neural network that can generalize to independent data sets. We also demonstrate that the methylation-associated genomic loci detected by the classifier are associated with genes, pathways and networks involved in cancer, providing insights into the epigenomic regulation of carcinogenesis.
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Affiliation(s)
- Izzy Newsham
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, United Kingdom
| | - Marcin Sendera
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom
- Jagiellonian University, Faculty of Mathematics and Computer Science, 30-348 Kraków, Poland
| | - Sri Ganesh Jammula
- CRUK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, United Kingdom
- MedGenome labs, Bengaluru, 560099, India
| | - Shamith A Samarajiwa
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom
- Imperial College London, Hammersmith Campus, London, W12 0NN, United Kingdom
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97
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Braune M, Metelmann M, de Fallois J, Pfrepper C, Barrantes-Freer A, Hiller GGR, Unger S, Seelow E, Halbritter J, Pelz JO. Imbalance of the von Willebrand Factor - ADAMTS-13 axis in patients with retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (RVCL-S). Neurol Res Pract 2024; 6:32. [PMID: 38898536 PMCID: PMC11188181 DOI: 10.1186/s42466-024-00327-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/08/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (RVCL-S) is an ultra-rare, autosomal-dominant small vessel disease caused by loss-of-function variants in the gene TREX1. Recently, elevated serum levels of von Willebrand Factor Antigen (vWF-Ag) pointed to an underlying endotheliopathy, and microvascular ischemia was suggested to contribute to the neurodegeneration in RVCL-S. Aim of this study was to further elucidate the endotheliopathy in RVCL-S. METHODS vWF-Ag and ADAMTS-13 activity were repeatedly measured in two patients with genetically confirmed RVCL-S. Renal biopsy of both RVCL-S patients and autoptic brain, renal, hepatic, and pulmonary specimen of one patient with RVCL-S were examined immunohistochemically in comparison to matched controls. In addition, cerebral methylome analysis was performed in the autoptic brain specimen calculating differentially methylated positions compared to controls. RESULTS While vWF-Ag and activity was strongly elevated, ADAMTS-13 activity was low in RVCL-S and further decreased over the course of the disease. Autoptic brain specimen showed signs of thromboinflammation in cerebral small vessels, and vWF-Ag staining was strongly positive in cerebral and renal small vessels in RVCL-S, while only a light to moderate vWF-Ag staining was found in controls. Cerebral methylome analysis yielded 115 differentially methylated CpGs (p < 0.05) in the deceased RVCL-S patient compared to the eight controls without brain pathology. One of the hypomethylated genes coded for ADAMTS-13 (p = 0.00056). CONCLUSIONS These findings point to an imbalance of the vWF - ADAMTS-13 axis in patients with RVCL-S, that may finally lead to an accumulation of vWF-Ag in renal and cerebral small vessels. Elevated vWF-Ag levels may serve as an early serum marker reflecting disease activity. If confirmed, therapeutic approaches might aim at an inhibition of vWF-Ag or increase of ADAMTS-13 activity in the future.
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Affiliation(s)
- Max Braune
- Paul-Flechsig-Institute for Neuropathology, University Hospital Leipzig, Leipzig, Germany
| | - Moritz Metelmann
- Department of Neurology, University Hospital Leipzig, Liebigstraße 20, Leipzig, 04103, Germany
| | | | - Christian Pfrepper
- Division of Haemostaseology, Medical Department I, University Hospital Leipzig, Leipzig, Germany
| | - Alonso Barrantes-Freer
- Paul-Flechsig-Institute for Neuropathology, University Hospital Leipzig, Leipzig, Germany
| | | | - Susette Unger
- Division of Rheumatology, Hospital St. Georg, Leipzig, Germany
| | - Evelyn Seelow
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Halbritter
- Division of Nephrology, University Hospital Leipzig, Leipzig, Germany.
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany.
| | - Johann Otto Pelz
- Department of Neurology, University Hospital Leipzig, Liebigstraße 20, Leipzig, 04103, Germany.
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98
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Vazaios K, Stavrakaki Ε, Vogelezang LB, Ju J, Waranecki P, Metselaar DS, Meel MH, Kemp V, van den Hoogen BG, Hoeben RC, Chiocca EA, Goins WF, Stubbs A, Li Y, Alonso MM, Calkoen FG, Hulleman E, van der Lugt J, Lamfers ML. The heterogeneous sensitivity of pediatric brain tumors to different oncolytic viruses is predicted by unique gene expression profiles. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200804. [PMID: 38694569 PMCID: PMC11060958 DOI: 10.1016/j.omton.2024.200804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/11/2024] [Indexed: 05/04/2024]
Abstract
Despite decades of research, the prognosis of high-grade pediatric brain tumors (PBTs) remains dismal; however, recent cases of favorable clinical responses were documented in clinical trials using oncolytic viruses (OVs). In the current study, we employed four different species of OVs: adenovirus Delta24-RGD, herpes simplex virus rQNestin34.5v1, reovirus R124, and the non-virulent Newcastle disease virus rNDV-F0-GFP against three entities of PBTs (high-grade gliomas, atypical teratoid/rhabdoid tumors, and ependymomas) to determine their in vitro efficacy. These four OVs were screened on 14 patient-derived PBT cell cultures and the degree of oncolysis was assessed using an ATP-based assay. Subsequently, the observed viral efficacies were correlated to whole transcriptome data and Gene Ontology analysis was performed. Although no significant tumor type-specific OV efficacy was observed, the analysis revealed the intrinsic biological processes that associated with OV efficacy. The predictive power of the identified expression profiles was further validated in vitro by screening additional PBTs. In summary, our results demonstrate OV susceptibility of multiple patient-derived PBT entities and the ability to predict in vitro responses to OVs using unique expression profiles. Such profiles may hold promise for future OV preselection with effective oncolytic potency in a specific tumor, therewith potentially improving OV responses.
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Affiliation(s)
- Konstantinos Vazaios
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Department of Neurosurgery, Brain Tumor Center, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Εftychia Stavrakaki
- Department of Neurosurgery, Brain Tumor Center, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Lisette B. Vogelezang
- Department of Neurosurgery, Brain Tumor Center, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Jie Ju
- Department of Pathology and Clinical Bioinformatics, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Piotr Waranecki
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Dennis S. Metselaar
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Michaël H. Meel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Vera Kemp
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | | | - Rob C. Hoeben
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - E. Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - William F. Goins
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Dr, Pittsburgh, PA 15219, USA
| | - Andrew Stubbs
- Department of Pathology and Clinical Bioinformatics, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Yunlei Li
- Department of Pathology and Clinical Bioinformatics, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Marta M. Alonso
- Program in Solid Tumors, Center for Applied Medical Research (CIMA), Avda. de Pío XII, 55, 31008 Pamplona, Spain
- Department of Pediatrics, Clínica Universidad de Navarra, Av. de Pío XII, 36, 31008 Pamplona, Spain
- Health Research Institute of Navarra (IDISNA), Av. de Pío XII, 36, 31008 Pamplona, Spain
| | - Friso G. Calkoen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Esther Hulleman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Jasper van der Lugt
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Martine L.M. Lamfers
- Department of Neurosurgery, Brain Tumor Center, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
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99
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Gue R, Lakhani DA. The 2021 World Health Organization Central Nervous System Tumor Classification: The Spectrum of Diffuse Gliomas. Biomedicines 2024; 12:1349. [PMID: 38927556 PMCID: PMC11202067 DOI: 10.3390/biomedicines12061349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The 2021 edition of the World Health Organization (WHO) classification of central nervous system tumors introduces significant revisions across various tumor types. These updates, encompassing changes in diagnostic techniques, genomic integration, terminology, and grading, are crucial for radiologists, who play a critical role in interpreting brain tumor imaging. Such changes impact the diagnosis and management of nearly all central nervous system tumor categories, including the reclassification, addition, and removal of specific tumor entities. Given their pivotal role in patient care, radiologists must remain conversant with these revisions to effectively contribute to multidisciplinary tumor boards and collaborate with peers in neuro-oncology, neurosurgery, radiation oncology, and neuropathology. This knowledge is essential not only for accurate diagnosis and staging, but also for understanding the molecular and genetic underpinnings of tumors, which can influence treatment decisions and prognostication. This review, therefore, focuses on the most pertinent updates concerning the classification of adult diffuse gliomas, highlighting the aspects most relevant to radiological practice. Emphasis is placed on the implications of new genetic information on tumor behavior and imaging findings, providing necessary tools to stay abreast of advancements in the field. This comprehensive overview aims to enhance the radiologist's ability to integrate new WHO classification criteria into everyday practice, ultimately improving patient outcomes through informed and precise imaging assessments.
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Affiliation(s)
- Racine Gue
- Department of Neuroradiology, West Virginia University, Morgantown, WV 26506, USA
| | - Dhairya A. Lakhani
- Department of Neuroradiology, West Virginia University, Morgantown, WV 26506, USA
- Department of Radiology and Radiological Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
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Han PC, Baker TG. Glial and glioneuronal tumors: Navigating the complexity of evolving concepts and new classification. J Neurol Sci 2024; 461:123058. [PMID: 38781807 DOI: 10.1016/j.jns.2024.123058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/25/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024]
Abstract
The World Health Organization (WHO) published the 5th edition classification of tumors of central nervous system in 2021, commonly abbreviated as WHO CNS5, which became the new standard for brain tumor diagnosis and therapy. This edition dramatically impacted tumor diagnostics. In short it introduced new tumors, changed the names of previously recognized tumors, and modified the working definition of previously known tumors. The new system appears complex due to the integration of morphological and multiple molecular criteria. The most radical changes occurred in the field of glial and glioneuronal tumors, which constitutes the lengthy first chapter of this new edition. Herein we present an illustrative outline of the evolving concepts of glial and glioneuronal tumors. We also attempt to explain the rationales behind this substantial change in tumor classification and the challenges to update and integrate it into clinical practice. We aim to present a concise and precise roadmap to aid navigation through the intricate conceptual framework of glial and glioneuronal tumors in the context of WHO CNS5.
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Affiliation(s)
- Peng Cheng Han
- Department of Pathology, Anatomy and Laboratory Medicine, Department of Neuroscience, West Virginia University, Morgantown, WV 26505, United States of America.
| | - Tiffany G Baker
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, United States of America
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